cmd.read_pdbstr("""\ HEADER IMMUNE SYSTEM/CHAPERONE 12-NOV-13 4NKO \ TITLE CRYSTAL STRUCTURE OF ENGINEERED ANTI-EE SCFV ANTIBODY FRAGMENT \ COMPND MOL_ID: 1; \ COMPND 2 MOLECULE: ENGINEERED SCFV; \ COMPND 3 CHAIN: A, B, C; \ COMPND 4 ENGINEERED: YES \ SOURCE MOL_ID: 1; \ SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; \ SOURCE 3 ORGANISM_COMMON: MOUSE; \ SOURCE 4 ORGANISM_TAXID: 10090; \ SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; \ SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 \ KEYWDS ANTIBODY FRAGMENT, HEXA-HISTIDINE BINDING, IMMUNE SYSTEM, IMMUNE \ KEYWDS 2 SYSTEM-CHAPERONE COMPLEX \ EXPDTA X-RAY DIFFRACTION \ AUTHOR S.KALYONCU,J.HYUN,J.C.PAI,J.L.JOHNSON,K.ETZMINGER,A.JAIN,D.HEANER \ AUTHOR 2 JR.,I.A.MOLARES,T.M.TRUSKETT,J.A.MAYNARD,R.L.LIEBERMAN \ REVDAT 7 16-OCT-24 4NKO 1 REMARK \ REVDAT 6 27-MAR-24 4NKO 1 COMPND SOURCE REMARK DBREF \ REVDAT 6 2 1 SEQRES HELIX SHEET SSBOND \ REVDAT 6 3 1 ATOM \ REVDAT 5 20-SEP-23 4NKO 1 REMARK \ REVDAT 4 22-NOV-17 4NKO 1 REMARK \ REVDAT 3 03-SEP-14 4NKO 1 JRNL \ REVDAT 2 09-APR-14 4NKO 1 JRNL \ REVDAT 1 12-MAR-14 4NKO 0 \ JRNL AUTH S.KALYONCU,J.HYUN,J.C.PAI,J.L.JOHNSON,K.ENTZMINGER,A.JAIN, \ JRNL AUTH 2 D.P.HEANER,I.A.MORALES,T.M.TRUSKETT,J.A.MAYNARD, \ JRNL AUTH 3 R.L.LIEBERMAN \ JRNL TITL EFFECTS OF PROTEIN ENGINEERING AND RATIONAL MUTAGENESIS ON \ JRNL TITL 2 CRYSTAL LATTICE OF SINGLE CHAIN ANTIBODY FRAGMENTS. \ JRNL REF PROTEINS V. 82 1884 2014 \ JRNL REFN ISSN 0887-3585 \ JRNL PMID 24615866 \ JRNL DOI 10.1002/PROT.24542 \ REMARK 2 \ REMARK 2 RESOLUTION. 3.50 ANGSTROMS. \ REMARK 3 \ REMARK 3 REFINEMENT. \ REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) \ REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN \ REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, \ REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, \ REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, \ REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, \ REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, \ REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT \ REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART \ REMARK 3 \ REMARK 3 REFINEMENT TARGET : ML \ REMARK 3 \ REMARK 3 DATA USED IN REFINEMENT. \ REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.50 \ REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.20 \ REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 \ REMARK 3 COMPLETENESS FOR RANGE (%) : NULL \ REMARK 3 NUMBER OF REFLECTIONS : 11014 \ REMARK 3 \ REMARK 3 FIT TO DATA USED IN REFINEMENT. \ REMARK 3 R VALUE (WORKING + TEST SET) : 0.310 \ REMARK 3 R VALUE (WORKING SET) : 0.308 \ REMARK 3 FREE R VALUE : 0.344 \ REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.720 \ REMARK 3 FREE R VALUE TEST SET COUNT : 520 \ REMARK 3 \ REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). \ REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE \ REMARK 3 1 42.2203 - 5.5463 0.95 2778 134 0.2786 0.2994 \ REMARK 3 2 5.5463 - 4.4038 0.97 2765 142 0.2904 0.3656 \ REMARK 3 3 4.4038 - 3.8475 0.87 2451 124 0.3427 0.3693 \ REMARK 3 4 3.8475 - 3.4960 0.90 2500 120 0.4259 0.4555 \ REMARK 3 \ REMARK 3 BULK SOLVENT MODELLING. \ REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL \ REMARK 3 SOLVENT RADIUS : 1.11 \ REMARK 3 SHRINKAGE RADIUS : 0.90 \ REMARK 3 K_SOL : NULL \ REMARK 3 B_SOL : NULL \ REMARK 3 \ REMARK 3 ERROR ESTIMATES. \ REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.670 \ REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 45.180 \ REMARK 3 \ REMARK 3 B VALUES. \ REMARK 3 FROM WILSON PLOT (A**2) : NULL \ REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL \ REMARK 3 OVERALL ANISOTROPIC B VALUE. \ REMARK 3 B11 (A**2) : NULL \ REMARK 3 B22 (A**2) : NULL \ REMARK 3 B33 (A**2) : NULL \ REMARK 3 B12 (A**2) : NULL \ REMARK 3 B13 (A**2) : NULL \ REMARK 3 B23 (A**2) : NULL \ REMARK 3 \ REMARK 3 TWINNING INFORMATION. \ REMARK 3 FRACTION: NULL \ REMARK 3 OPERATOR: NULL \ REMARK 3 \ REMARK 3 DEVIATIONS FROM IDEAL VALUES. \ REMARK 3 RMSD COUNT \ REMARK 3 BOND : 0.004 5522 \ REMARK 3 ANGLE : 1.249 7473 \ REMARK 3 CHIRALITY : 0.046 807 \ REMARK 3 PLANARITY : 0.005 963 \ REMARK 3 DIHEDRAL : 14.516 2007 \ REMARK 3 \ REMARK 3 TLS DETAILS \ REMARK 3 NUMBER OF TLS GROUPS : NULL \ REMARK 3 \ REMARK 3 NCS DETAILS \ REMARK 3 NUMBER OF NCS GROUPS : 2 \ REMARK 3 NCS GROUP : 1 \ REMARK 3 NCS GROUP : 2 \ REMARK 3 NCS OPERATOR : 1 \ REMARK 3 REFERENCE SELECTION: NULL \ REMARK 3 SELECTION : NULL \ REMARK 3 ATOM PAIRS NUMBER : NULL \ REMARK 3 RMSD : NULL \ REMARK 3 \ REMARK 3 OTHER REFINEMENT REMARKS: NULL \ REMARK 4 \ REMARK 4 4NKO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 \ REMARK 100 \ REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-DEC-13. \ REMARK 100 THE DEPOSITION ID IS D_1000083323. \ REMARK 200 \ REMARK 200 EXPERIMENTAL DETAILS \ REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION \ REMARK 200 DATE OF DATA COLLECTION : 04-NOV-11 \ REMARK 200 TEMPERATURE (KELVIN) : 100 \ REMARK 200 PH : 6 \ REMARK 200 NUMBER OF CRYSTALS USED : 1 \ REMARK 200 \ REMARK 200 SYNCHROTRON (Y/N) : Y \ REMARK 200 RADIATION SOURCE : APS \ REMARK 200 BEAMLINE : 22-ID \ REMARK 200 X-RAY GENERATOR MODEL : NULL \ REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M \ REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 \ REMARK 200 MONOCHROMATOR : ROSENBAUM-ROCK MONOCHROMATOR \ REMARK 200 HIGH-RESOLUTION DOUBLE-CRYSTAL \ REMARK 200 SI(220) SAGITTAL FOCUSING, \ REMARK 200 ROSENBAUM-ROCK VERTICAL FOCUSING \ REMARK 200 MIRROR \ REMARK 200 OPTICS : NULL \ REMARK 200 \ REMARK 200 DETECTOR TYPE : CCD \ REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD \ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 \ REMARK 200 DATA SCALING SOFTWARE : HKL-2000 \ REMARK 200 \ REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11089 \ REMARK 200 RESOLUTION RANGE HIGH (A) : 3.490 \ REMARK 200 RESOLUTION RANGE LOW (A) : 42.200 \ REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 \ REMARK 200 \ REMARK 200 OVERALL. \ REMARK 200 COMPLETENESS FOR RANGE (%) : 93.1 \ REMARK 200 DATA REDUNDANCY : NULL \ REMARK 200 R MERGE (I) : NULL \ REMARK 200 R SYM (I) : NULL \ REMARK 200 FOR THE DATA SET : 12.0000 \ REMARK 200 \ REMARK 200 IN THE HIGHEST RESOLUTION SHELL. \ REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.49 \ REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.62 \ REMARK 200 COMPLETENESS FOR SHELL (%) : 95.2 \ REMARK 200 DATA REDUNDANCY IN SHELL : NULL \ REMARK 200 R MERGE FOR SHELL (I) : NULL \ REMARK 200 R SYM FOR SHELL (I) : NULL \ REMARK 200 FOR SHELL : 2.970 \ REMARK 200 \ REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH \ REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT \ REMARK 200 SOFTWARE USED: PHASER \ REMARK 200 STARTING MODEL: PDB ENTRY 1KTR \ REMARK 200 \ REMARK 200 REMARK: NULL \ REMARK 280 \ REMARK 280 CRYSTAL \ REMARK 280 SOLVENT CONTENT, VS (%): 53.34 \ REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 \ REMARK 280 \ REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS OF 3D5/HIS_683 (8MG/ML IN \ REMARK 280 HBS) WERE GROWN AT ROOM TEMPERATURE WITH 0.2M KI, 0.001M \ REMARK 280 GUANIDINIUM HCL, 18% PEG 8000. THESE CRYSTALS APPEARED IN 2-3 \ REMARK 280 DAYS., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298.15K, PH 6 \ REMARK 290 \ REMARK 290 CRYSTALLOGRAPHIC SYMMETRY \ REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 \ REMARK 290 \ REMARK 290 SYMOP SYMMETRY \ REMARK 290 NNNMMM OPERATOR \ REMARK 290 1555 X,Y,Z \ REMARK 290 2555 -X,-Y,Z+1/2 \ REMARK 290 3555 -X,Y,-Z+1/2 \ REMARK 290 4555 X,-Y,-Z \ REMARK 290 5555 X+1/2,Y+1/2,Z \ REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 \ REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 \ REMARK 290 8555 X+1/2,-Y+1/2,-Z \ REMARK 290 \ REMARK 290 WHERE NNN -> OPERATOR NUMBER \ REMARK 290 MMM -> TRANSLATION VECTOR \ REMARK 290 \ REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS \ REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM \ REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY \ REMARK 290 RELATED MOLECULES. \ REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 \ REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 \ REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 \ REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 \ REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 \ REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 142.20650 \ REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 \ REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 \ REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 142.20650 \ REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 \ REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 \ REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 \ REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 30.29300 \ REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 52.45850 \ REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 \ REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 30.29300 \ REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 52.45850 \ REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 142.20650 \ REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 30.29300 \ REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 52.45850 \ REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 142.20650 \ REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 30.29300 \ REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 52.45850 \ REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 \ REMARK 290 \ REMARK 290 REMARK: NULL \ REMARK 300 \ REMARK 300 BIOMOLECULE: 1, 2, 3 \ REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM \ REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN \ REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON \ REMARK 300 BURIED SURFACE AREA. \ REMARK 350 \ REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN \ REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE \ REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS \ REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND \ REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. \ REMARK 350 \ REMARK 350 BIOMOLECULE: 1 \ REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC \ REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC \ REMARK 350 SOFTWARE USED: PISA \ REMARK 350 TOTAL BURIED SURFACE AREA: 1560 ANGSTROM**2 \ REMARK 350 SURFACE AREA OF THE COMPLEX: 11570 ANGSTROM**2 \ REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL \ REMARK 350 APPLY THE FOLLOWING TO CHAINS: A \ REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 \ REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 \ REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 \ REMARK 350 \ REMARK 350 BIOMOLECULE: 2 \ REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC \ REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC \ REMARK 350 SOFTWARE USED: PISA \ REMARK 350 TOTAL BURIED SURFACE AREA: 1510 ANGSTROM**2 \ REMARK 350 SURFACE AREA OF THE COMPLEX: 11600 ANGSTROM**2 \ REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL \ REMARK 350 APPLY THE FOLLOWING TO CHAINS: B \ REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 \ REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 \ REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 \ REMARK 350 \ REMARK 350 BIOMOLECULE: 3 \ REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC \ REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC \ REMARK 350 SOFTWARE USED: PISA \ REMARK 350 TOTAL BURIED SURFACE AREA: 1550 ANGSTROM**2 \ REMARK 350 SURFACE AREA OF THE COMPLEX: 11490 ANGSTROM**2 \ REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL \ REMARK 350 APPLY THE FOLLOWING TO CHAINS: C \ REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 \ REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 \ REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 \ REMARK 465 \ REMARK 465 MISSING RESIDUES \ REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE \ REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN \ REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) \ REMARK 465 \ REMARK 465 M RES C SSSEQI \ REMARK 465 MET A -4 \ REMARK 465 ALA A -3 \ REMARK 465 ASP A -2 \ REMARK 465 TYR A -1 \ REMARK 465 LYS A 0 \ REMARK 465 GLY A 116 \ REMARK 465 GLY A 117 \ REMARK 465 SER A 118 \ REMARK 465 GLY A 119 \ REMARK 465 GLY A 120 \ REMARK 465 GLY A 121 \ REMARK 465 GLY A 122 \ REMARK 465 SER A 123 \ REMARK 465 GLY A 124 \ REMARK 465 GLY A 125 \ REMARK 465 GLY A 126 \ REMARK 465 GLY A 127 \ REMARK 465 SER A 128 \ REMARK 465 SER A 129 \ REMARK 465 GLY A 130 \ REMARK 465 GLY A 131 \ REMARK 465 GLY A 132 \ REMARK 465 SER A 133 \ REMARK 465 SER A 255 \ REMARK 465 GLY A 256 \ REMARK 465 ALA A 257 \ REMARK 465 ASP A 258 \ REMARK 465 HIS A 259 \ REMARK 465 HIS A 260 \ REMARK 465 HIS A 261 \ REMARK 465 HIS A 262 \ REMARK 465 HIS A 263 \ REMARK 465 HIS A 264 \ REMARK 465 MET B -4 \ REMARK 465 ALA B -3 \ REMARK 465 ASP B -2 \ REMARK 465 TYR B -1 \ REMARK 465 LYS B 0 \ REMARK 465 GLY B 116 \ REMARK 465 GLY B 117 \ REMARK 465 SER B 118 \ REMARK 465 GLY B 119 \ REMARK 465 GLY B 120 \ REMARK 465 GLY B 121 \ REMARK 465 GLY B 122 \ REMARK 465 SER B 123 \ REMARK 465 GLY B 124 \ REMARK 465 GLY B 125 \ REMARK 465 GLY B 126 \ REMARK 465 GLY B 127 \ REMARK 465 SER B 128 \ REMARK 465 SER B 129 \ REMARK 465 GLY B 130 \ REMARK 465 GLY B 131 \ REMARK 465 GLY B 132 \ REMARK 465 SER B 133 \ REMARK 465 SER B 255 \ REMARK 465 GLY B 256 \ REMARK 465 ALA B 257 \ REMARK 465 ASP B 258 \ REMARK 465 HIS B 259 \ REMARK 465 HIS B 260 \ REMARK 465 HIS B 261 \ REMARK 465 HIS B 262 \ REMARK 465 HIS B 263 \ REMARK 465 HIS B 264 \ REMARK 465 MET C -4 \ REMARK 465 ALA C -3 \ REMARK 465 ASP C -2 \ REMARK 465 TYR C -1 \ REMARK 465 LYS C 0 \ REMARK 465 GLY C 116 \ REMARK 465 GLY C 117 \ REMARK 465 SER C 118 \ REMARK 465 GLY C 119 \ REMARK 465 GLY C 120 \ REMARK 465 GLY C 121 \ REMARK 465 GLY C 122 \ REMARK 465 SER C 123 \ REMARK 465 GLY C 124 \ REMARK 465 GLY C 125 \ REMARK 465 GLY C 126 \ REMARK 465 GLY C 127 \ REMARK 465 SER C 128 \ REMARK 465 SER C 129 \ REMARK 465 GLY C 130 \ REMARK 465 GLY C 131 \ REMARK 465 GLY C 132 \ REMARK 465 SER C 133 \ REMARK 465 SER C 255 \ REMARK 465 GLY C 256 \ REMARK 465 ALA C 257 \ REMARK 465 ASP C 258 \ REMARK 465 HIS C 259 \ REMARK 465 HIS C 260 \ REMARK 465 HIS C 261 \ REMARK 465 HIS C 262 \ REMARK 465 HIS C 263 \ REMARK 465 HIS C 264 \ REMARK 500 \ REMARK 500 GEOMETRY AND STEREOCHEMISTRY \ REMARK 500 SUBTOPIC: COVALENT BOND ANGLES \ REMARK 500 \ REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES \ REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE \ REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN \ REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). \ REMARK 500 \ REMARK 500 STANDARD TABLE: \ REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) \ REMARK 500 \ REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 \ REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 \ REMARK 500 \ REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 \ REMARK 500 PRO A 12 C - N - CA ANGL. DEV. = 9.4 DEGREES \ REMARK 500 PRO C 12 C - N - CA ANGL. DEV. = 14.5 DEGREES \ REMARK 500 \ REMARK 500 REMARK: NULL \ REMARK 500 \ REMARK 500 GEOMETRY AND STEREOCHEMISTRY \ REMARK 500 SUBTOPIC: TORSION ANGLES \ REMARK 500 \ REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: \ REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; \ REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). \ REMARK 500 \ REMARK 500 STANDARD TABLE: \ REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) \ REMARK 500 \ REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- \ REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 \ REMARK 500 \ REMARK 500 M RES CSSEQI PSI PHI \ REMARK 500 LEU A 52 -60.67 -107.64 \ REMARK 500 LYS A 55 70.62 54.47 \ REMARK 500 VAL A 56 -102.89 65.26 \ REMARK 500 PRO A 147 92.04 -57.12 \ REMARK 500 ASN A 187 -72.27 -59.17 \ REMARK 500 ARG A 217 -74.09 -101.27 \ REMARK 500 ALA A 231 -58.95 -128.06 \ REMARK 500 SER A 233 -163.29 -128.09 \ REMARK 500 TYR A 235 80.87 35.96 \ REMARK 500 SER A 236 142.20 -36.06 \ REMARK 500 ARG A 238 160.99 179.29 \ REMARK 500 ALA A 240 77.88 62.42 \ REMARK 500 TRP A 244 40.34 71.58 \ REMARK 500 LEU B 52 -60.53 -108.71 \ REMARK 500 VAL B 56 -103.01 64.77 \ REMARK 500 ASN B 187 -72.10 -58.16 \ REMARK 500 ARG B 217 -73.17 -101.51 \ REMARK 500 ALA B 231 -58.83 -127.84 \ REMARK 500 TYR B 235 68.50 34.09 \ REMARK 500 SER B 236 84.09 51.66 \ REMARK 500 ALA B 240 77.97 61.80 \ REMARK 500 TRP B 244 39.98 71.75 \ REMARK 500 LEU C 52 -61.11 -109.97 \ REMARK 500 VAL C 56 -45.09 67.55 \ REMARK 500 ASN C 187 -71.98 -58.82 \ REMARK 500 ARG C 217 -72.99 -101.77 \ REMARK 500 ALA C 231 -58.23 -128.03 \ REMARK 500 TYR C 235 68.77 34.17 \ REMARK 500 SER C 236 79.56 57.69 \ REMARK 500 ALA C 240 78.05 61.84 \ REMARK 500 TRP C 244 40.35 71.65 \ REMARK 500 \ REMARK 500 REMARK: NULL \ REMARK 900 \ REMARK 900 RELATED ENTRIES \ REMARK 900 RELATED ID: 3NN8 RELATED DB: PDB \ REMARK 900 CRYSTAL STRUCTURE OF ENGINEERED ANTIBODY FRAGMENT BASED ON 3D5 \ REMARK 900 RELATED ID: 1KTR RELATED DB: PDB \ REMARK 900 ANTI-HIS TAG ANTIBODY 3D5 SINGLE-CHAIN FRAGMENT (SCFV) IN COMPLEX \ REMARK 900 WITH A OLIGOHISTIDINE PEPTIDE \ REMARK 900 RELATED ID: 4NKD RELATED DB: PDB \ REMARK 900 CRYSTAL STRUCTURE OF ENGINEERED ANTI-EE SCFV ANTIBODY FRAGMENT \ REMARK 900 RELATED ID: 4NKM RELATED DB: PDB \ REMARK 900 CRYSTAL STRUCTURE OF ENGINEERED ANTI-EE SCFV ANTIBODY FRAGMENT \ DBREF 4NKO A -4 264 PDB 4NKO 4NKO -4 264 \ DBREF 4NKO B -4 264 PDB 4NKO 4NKO -4 264 \ DBREF 4NKO C -4 264 PDB 4NKO 4NKO -4 264 \ SEQRES 1 A 269 MET ALA ASP TYR LYS ASP ILE VAL MET THR GLN THR PRO \ SEQRES 2 A 269 SER SER LEU PRO VAL SER LEU GLY ASP GLN ALA SER ILE \ SEQRES 3 A 269 SER CYS ARG SER SER GLN SER ILE VAL HIS SER ASN GLY \ SEQRES 4 A 269 ASN THR TYR LEU GLU TRP TYR LEU GLN LYS PRO GLY GLN \ SEQRES 5 A 269 SER PRO LYS LEU LEU ILE TYR LYS VAL SER ASN ARG PHE \ SEQRES 6 A 269 SER GLY VAL PRO ASP ARG PHE SER GLY SER GLY SER GLY \ SEQRES 7 A 269 THR ASP PHE THR LEU LYS ILE SER ARG VAL GLU ALA GLU \ SEQRES 8 A 269 ASP LEU GLY ILE TYR TYR CYS PHE GLN GLY SER LEU VAL \ SEQRES 9 A 269 PRO PRO THR PHE GLY ALA GLY THR LYS LEU GLU LEU LYS \ SEQRES 10 A 269 ARG GLY GLY GLY GLY SER GLY GLY GLY GLY SER GLY GLY \ SEQRES 11 A 269 GLY GLY SER SER GLY GLY GLY SER GLN VAL GLN LEU GLN \ SEQRES 12 A 269 GLN SER GLY PRO GLU ASP VAL LYS PRO GLY ALA SER VAL \ SEQRES 13 A 269 LYS ILE SER CYS LYS ALA SER GLY TYR THR PHE THR ASP \ SEQRES 14 A 269 TYR TYR MET ASN TRP VAL LYS GLN SER PRO GLY LYS GLY \ SEQRES 15 A 269 LEU GLU TRP ILE GLY ASP ILE ASN PRO ASN ASN GLY GLY \ SEQRES 16 A 269 THR SER TYR ASN GLN LYS PHE LYS GLY ARG ALA THR LEU \ SEQRES 17 A 269 THR VAL ASP LYS SER SER SER THR ALA TYR MET GLU LEU \ SEQRES 18 A 269 ARG SER LEU THR SER GLU ASP SER SER VAL TYR TYR CYS \ SEQRES 19 A 269 ALA ALA SER SER PRO TYR SER MET ARG ALA ALA MET ASP \ SEQRES 20 A 269 TYR TRP GLY GLN GLY THR THR VAL THR VAL SER ALA SER \ SEQRES 21 A 269 GLY ALA ASP HIS HIS HIS HIS HIS HIS \ SEQRES 1 B 269 MET ALA ASP TYR LYS ASP ILE VAL MET THR GLN THR PRO \ SEQRES 2 B 269 SER SER LEU PRO VAL SER LEU GLY ASP GLN ALA SER ILE \ SEQRES 3 B 269 SER CYS ARG SER SER GLN SER ILE VAL HIS SER ASN GLY \ SEQRES 4 B 269 ASN THR TYR LEU GLU TRP TYR LEU GLN LYS PRO GLY GLN \ SEQRES 5 B 269 SER PRO LYS LEU LEU ILE TYR LYS VAL SER ASN ARG PHE \ SEQRES 6 B 269 SER GLY VAL PRO ASP ARG PHE SER GLY SER GLY SER GLY \ SEQRES 7 B 269 THR ASP PHE THR LEU LYS ILE SER ARG VAL GLU ALA GLU \ SEQRES 8 B 269 ASP LEU GLY ILE TYR TYR CYS PHE GLN GLY SER LEU VAL \ SEQRES 9 B 269 PRO PRO THR PHE GLY ALA GLY THR LYS LEU GLU LEU LYS \ SEQRES 10 B 269 ARG GLY GLY GLY GLY SER GLY GLY GLY GLY SER GLY GLY \ SEQRES 11 B 269 GLY GLY SER SER GLY GLY GLY SER GLN VAL GLN LEU GLN \ SEQRES 12 B 269 GLN SER GLY PRO GLU ASP VAL LYS PRO GLY ALA SER VAL \ SEQRES 13 B 269 LYS ILE SER CYS LYS ALA SER GLY TYR THR PHE THR ASP \ SEQRES 14 B 269 TYR TYR MET ASN TRP VAL LYS GLN SER PRO GLY LYS GLY \ SEQRES 15 B 269 LEU GLU TRP ILE GLY ASP ILE ASN PRO ASN ASN GLY GLY \ SEQRES 16 B 269 THR SER TYR ASN GLN LYS PHE LYS GLY ARG ALA THR LEU \ SEQRES 17 B 269 THR VAL ASP LYS SER SER SER THR ALA TYR MET GLU LEU \ SEQRES 18 B 269 ARG SER LEU THR SER GLU ASP SER SER VAL TYR TYR CYS \ SEQRES 19 B 269 ALA ALA SER SER PRO TYR SER MET ARG ALA ALA MET ASP \ SEQRES 20 B 269 TYR TRP GLY GLN GLY THR THR VAL THR VAL SER ALA SER \ SEQRES 21 B 269 GLY ALA ASP HIS HIS HIS HIS HIS HIS \ SEQRES 1 C 269 MET ALA ASP TYR LYS ASP ILE VAL MET THR GLN THR PRO \ SEQRES 2 C 269 SER SER LEU PRO VAL SER LEU GLY ASP GLN ALA SER ILE \ SEQRES 3 C 269 SER CYS ARG SER SER GLN SER ILE VAL HIS SER ASN GLY \ SEQRES 4 C 269 ASN THR TYR LEU GLU TRP TYR LEU GLN LYS PRO GLY GLN \ SEQRES 5 C 269 SER PRO LYS LEU LEU ILE TYR LYS VAL SER ASN ARG PHE \ SEQRES 6 C 269 SER GLY VAL PRO ASP ARG PHE SER GLY SER GLY SER GLY \ SEQRES 7 C 269 THR ASP PHE THR LEU LYS ILE SER ARG VAL GLU ALA GLU \ SEQRES 8 C 269 ASP LEU GLY ILE TYR TYR CYS PHE GLN GLY SER LEU VAL \ SEQRES 9 C 269 PRO PRO THR PHE GLY ALA GLY THR LYS LEU GLU LEU LYS \ SEQRES 10 C 269 ARG GLY GLY GLY GLY SER GLY GLY GLY GLY SER GLY GLY \ SEQRES 11 C 269 GLY GLY SER SER GLY GLY GLY SER GLN VAL GLN LEU GLN \ SEQRES 12 C 269 GLN SER GLY PRO GLU ASP VAL LYS PRO GLY ALA SER VAL \ SEQRES 13 C 269 LYS ILE SER CYS LYS ALA SER GLY TYR THR PHE THR ASP \ SEQRES 14 C 269 TYR TYR MET ASN TRP VAL LYS GLN SER PRO GLY LYS GLY \ SEQRES 15 C 269 LEU GLU TRP ILE GLY ASP ILE ASN PRO ASN ASN GLY GLY \ SEQRES 16 C 269 THR SER TYR ASN GLN LYS PHE LYS GLY ARG ALA THR LEU \ SEQRES 17 C 269 THR VAL ASP LYS SER SER SER THR ALA TYR MET GLU LEU \ SEQRES 18 C 269 ARG SER LEU THR SER GLU ASP SER SER VAL TYR TYR CYS \ SEQRES 19 C 269 ALA ALA SER SER PRO TYR SER MET ARG ALA ALA MET ASP \ SEQRES 20 C 269 TYR TRP GLY GLN GLY THR THR VAL THR VAL SER ALA SER \ SEQRES 21 C 269 GLY ALA ASP HIS HIS HIS HIS HIS HIS \ HELIX 1 1 GLU A 84 LEU A 88 5 5 \ HELIX 2 2 THR A 161 TYR A 165 5 5 \ HELIX 3 3 GLU B 84 LEU B 88 5 5 \ HELIX 4 4 GLU C 84 LEU C 88 5 5 \ HELIX 5 5 THR C 161 TYR C 165 5 5 \ SHEET 1 A 4 MET A 4 THR A 7 0 \ SHEET 2 A 4 ALA A 19 SER A 25 -1 O SER A 22 N THR A 7 \ SHEET 3 A 4 ASP A 75 ILE A 80 -1 O PHE A 76 N CYS A 23 \ SHEET 4 A 4 PHE A 67 GLY A 71 -1 N SER A 68 O LYS A 79 \ SHEET 1 B 6 SER A 10 PRO A 12 0 \ SHEET 2 B 6 THR A 107 GLU A 110 1 O GLU A 110 N LEU A 11 \ SHEET 3 B 6 GLY A 89 GLN A 95 -1 N TYR A 91 O THR A 107 \ SHEET 4 B 6 LEU A 38 GLN A 43 -1 N GLU A 39 O PHE A 94 \ SHEET 5 B 6 LYS A 50 TYR A 54 -1 O LEU A 52 N TRP A 40 \ SHEET 6 B 6 ASN A 58 ARG A 59 -1 O ASN A 58 N TYR A 54 \ SHEET 1 C 4 SER A 10 PRO A 12 0 \ SHEET 2 C 4 THR A 107 GLU A 110 1 O GLU A 110 N LEU A 11 \ SHEET 3 C 4 GLY A 89 GLN A 95 -1 N TYR A 91 O THR A 107 \ SHEET 4 C 4 THR A 102 PHE A 103 -1 O THR A 102 N GLN A 95 \ SHEET 1 D 4 GLN A 136 GLN A 139 0 \ SHEET 2 D 4 VAL A 151 SER A 158 -1 O SER A 158 N GLN A 136 \ SHEET 3 D 4 THR A 211 LEU A 216 -1 O MET A 214 N ILE A 153 \ SHEET 4 D 4 ALA A 201 ASP A 206 -1 N ASP A 206 O THR A 211 \ SHEET 1 E 6 GLU A 143 VAL A 145 0 \ SHEET 2 E 6 THR A 248 VAL A 252 1 O THR A 251 N GLU A 143 \ SHEET 3 E 6 SER A 225 ALA A 230 -1 N SER A 225 O VAL A 250 \ SHEET 4 E 6 MET A 167 SER A 173 -1 N GLN A 172 O VAL A 226 \ SHEET 5 E 6 GLY A 177 ILE A 184 -1 O ILE A 181 N TRP A 169 \ SHEET 6 E 6 SER A 192 TYR A 193 -1 O SER A 192 N ASP A 183 \ SHEET 1 F 4 THR B 5 THR B 7 0 \ SHEET 2 F 4 ALA B 19 ARG B 24 -1 O SER B 22 N THR B 7 \ SHEET 3 F 4 ASP B 75 ILE B 80 -1 O PHE B 76 N CYS B 23 \ SHEET 4 F 4 PHE B 67 GLY B 71 -1 N SER B 68 O LYS B 79 \ SHEET 1 G 6 SER B 10 PRO B 12 0 \ SHEET 2 G 6 THR B 107 GLU B 110 1 O LYS B 108 N LEU B 11 \ SHEET 3 G 6 GLY B 89 GLN B 95 -1 N TYR B 91 O THR B 107 \ SHEET 4 G 6 LEU B 38 GLN B 43 -1 N GLU B 39 O PHE B 94 \ SHEET 5 G 6 LYS B 50 TYR B 54 -1 O LEU B 52 N TRP B 40 \ SHEET 6 G 6 ASN B 58 ARG B 59 -1 O ASN B 58 N TYR B 54 \ SHEET 1 H 4 SER B 10 PRO B 12 0 \ SHEET 2 H 4 THR B 107 GLU B 110 1 O LYS B 108 N LEU B 11 \ SHEET 3 H 4 GLY B 89 GLN B 95 -1 N TYR B 91 O THR B 107 \ SHEET 4 H 4 THR B 102 PHE B 103 -1 O THR B 102 N GLN B 95 \ SHEET 1 I 4 GLN B 136 GLN B 139 0 \ SHEET 2 I 4 VAL B 151 SER B 158 -1 O SER B 158 N GLN B 136 \ SHEET 3 I 4 THR B 211 LEU B 216 -1 O ALA B 212 N CYS B 155 \ SHEET 4 I 4 ALA B 201 ASP B 206 -1 N ASP B 206 O THR B 211 \ SHEET 1 J 6 GLU B 143 VAL B 145 0 \ SHEET 2 J 6 THR B 248 VAL B 252 1 O THR B 251 N GLU B 143 \ SHEET 3 J 6 SER B 225 ALA B 230 -1 N SER B 225 O VAL B 250 \ SHEET 4 J 6 MET B 167 SER B 173 -1 N GLN B 172 O VAL B 226 \ SHEET 5 J 6 GLY B 177 ASN B 185 -1 O ILE B 184 N MET B 167 \ SHEET 6 J 6 GLY B 190 TYR B 193 -1 O SER B 192 N ASP B 183 \ SHEET 1 K 4 MET C 4 THR C 7 0 \ SHEET 2 K 4 ALA C 19 SER C 25 -1 O SER C 22 N THR C 7 \ SHEET 3 K 4 ASP C 75 ILE C 80 -1 O PHE C 76 N CYS C 23 \ SHEET 4 K 4 PHE C 67 GLY C 71 -1 N SER C 68 O LYS C 79 \ SHEET 1 L 6 SER C 10 PRO C 12 0 \ SHEET 2 L 6 THR C 107 GLU C 110 1 O GLU C 110 N LEU C 11 \ SHEET 3 L 6 GLY C 89 GLN C 95 -1 N GLY C 89 O LEU C 109 \ SHEET 4 L 6 LEU C 38 GLN C 43 -1 N GLN C 43 O ILE C 90 \ SHEET 5 L 6 PRO C 49 TYR C 54 -1 O LEU C 52 N TRP C 40 \ SHEET 6 L 6 ASN C 58 ARG C 59 -1 O ASN C 58 N TYR C 54 \ SHEET 1 M 4 SER C 10 PRO C 12 0 \ SHEET 2 M 4 THR C 107 GLU C 110 1 O GLU C 110 N LEU C 11 \ SHEET 3 M 4 GLY C 89 GLN C 95 -1 N GLY C 89 O LEU C 109 \ SHEET 4 M 4 THR C 102 PHE C 103 -1 O THR C 102 N GLN C 95 \ SHEET 1 N 4 GLN C 136 GLN C 139 0 \ SHEET 2 N 4 VAL C 151 SER C 158 -1 O SER C 158 N GLN C 136 \ SHEET 3 N 4 THR C 211 LEU C 216 -1 O ALA C 212 N CYS C 155 \ SHEET 4 N 4 ALA C 201 ASP C 206 -1 N ASP C 206 O THR C 211 \ SHEET 1 O 6 GLU C 143 VAL C 145 0 \ SHEET 2 O 6 THR C 248 VAL C 252 1 O THR C 251 N GLU C 143 \ SHEET 3 O 6 SER C 225 ALA C 230 -1 N SER C 225 O VAL C 250 \ SHEET 4 O 6 MET C 167 GLN C 172 -1 N GLN C 172 O VAL C 226 \ SHEET 5 O 6 LEU C 178 ILE C 184 -1 O ILE C 181 N TRP C 169 \ SHEET 6 O 6 SER C 192 TYR C 193 -1 O SER C 192 N ASP C 183 \ SSBOND 1 CYS A 23 CYS A 93 1555 1555 2.04 \ SSBOND 2 CYS B 23 CYS B 93 1555 1555 2.04 \ SSBOND 3 CYS B 155 CYS B 229 1555 1555 2.04 \ SSBOND 4 CYS C 23 CYS C 93 1555 1555 2.04 \ SSBOND 5 CYS C 155 CYS C 229 1555 1555 2.04 \ CISPEP 1 THR A 7 PRO A 8 0 -3.49 \ CISPEP 2 VAL A 99 PRO A 100 0 -5.34 \ CISPEP 3 SER A 233 PRO A 234 0 8.52 \ CISPEP 4 TYR A 243 TRP A 244 0 10.91 \ CISPEP 5 THR B 7 PRO B 8 0 -3.24 \ CISPEP 6 VAL B 99 PRO B 100 0 -5.56 \ CISPEP 7 SER B 233 PRO B 234 0 8.59 \ CISPEP 8 TYR B 243 TRP B 244 0 11.60 \ CISPEP 9 THR C 7 PRO C 8 0 -4.52 \ CISPEP 10 VAL C 99 PRO C 100 0 -6.04 \ CISPEP 11 SER C 233 PRO C 234 0 8.53 \ CISPEP 12 TYR C 243 TRP C 244 0 11.88 \ CRYST1 60.586 104.917 284.413 90.00 90.00 90.00 C 2 2 21 24 \ ORIGX1 1.000000 0.000000 0.000000 0.00000 \ ORIGX2 0.000000 1.000000 0.000000 0.00000 \ ORIGX3 0.000000 0.000000 1.000000 0.00000 \ SCALE1 0.016505 0.000000 0.000000 0.00000 \ SCALE2 0.000000 0.009531 0.000000 0.00000 \ SCALE3 0.000000 0.000000 0.003516 0.00000 \ TER 1799 ALA A 254 \ TER 3598 ALA B 254 \ TER 5397 ALA C 254 \ CONECT 161 715 \ CONECT 715 161 \ CONECT 1960 2514 \ CONECT 2514 1960 \ CONECT 2832 3416 \ CONECT 3416 2832 \ CONECT 3759 4313 \ CONECT 4313 3759 \ CONECT 4631 5215 \ CONECT 5215 4631 \ MASTER 433 0 0 5 72 0 0 6 5394 3 10 63 \ END \ """, "4nkochainF") cmd.hide("all") cmd.color('grey70', "4nkochainF") cmd.show('cartoon', "4nkochainF") cmd.center("4nkochainF", state=0, origin=1) cmd.zoom("4nkochainF", animate=-1) cmd.select("e4nkoF1", "c. F & i. 1-121") cmd.color("red", "e4nkoF1") cmd.disable("e4nkoF1")