cmd.read_pdbstr("""\ HEADER RIBOSOMAL PROTEIN 23-JUL-10 3IYX \ TITLE COORDINATES OF THE B1B BRIDGE-FORMING PROTEIN STRUCTURES FITTED INTO \ TITLE 2 THE CRYO-EM MAP OF E.COLI 70S RIBOSOME (EMD-1056) \ COMPND MOL_ID: 1; \ COMPND 2 MOLECULE: 30S RIBOSOMAL PROTEIN S13; \ COMPND 3 CHAIN: M; \ COMPND 4 MOL_ID: 2; \ COMPND 5 MOLECULE: 50S RIBOSOMAL PROTEIN L5; \ COMPND 6 CHAIN: F; \ COMPND 7 MOL_ID: 3; \ COMPND 8 MOLECULE: 50S RIBOSOMAL PROTEIN L31; \ COMPND 9 CHAIN: A \ SOURCE MOL_ID: 1; \ SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; \ SOURCE 3 ORGANISM_TAXID: 701177; \ SOURCE 4 STRAIN: O55:H7; \ SOURCE 5 MOL_ID: 2; \ SOURCE 6 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; \ SOURCE 7 ORGANISM_TAXID: 701177; \ SOURCE 8 STRAIN: O55:H7; \ SOURCE 9 MOL_ID: 3; \ SOURCE 10 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; \ SOURCE 11 ORGANISM_TAXID: 701177; \ SOURCE 12 STRAIN: O55:H7 \ KEYWDS RIBOSOMAL INTERSUBUNIT BRIDGES, B1B-BRIDGE, RATCHET-LIKE MOTION, \ KEYWDS 2 RIBOSOMAL PROTEIN L31, RIBOSOMAL PROTEIN \ EXPDTA ELECTRON MICROSCOPY \ MDLTYP CA ATOMS ONLY, CHAIN M, F, A \ AUTHOR M.SHASMAL,B.CHAKRABORTY,J.SENGUPTA \ REVDAT 4 21-FEB-24 3IYX 1 REMARK \ REVDAT 3 18-DEC-19 3IYX 1 CRYST1 SCALE \ REVDAT 2 18-JUL-18 3IYX 1 REMARK \ REVDAT 1 01-SEP-10 3IYX 0 \ JRNL AUTH M.SHASMAL,B.CHAKRABORTY,J.SENGUPTA \ JRNL TITL INTRINSIC MOLECULAR PROPERTIES OF THE PROTEIN-PROTEIN BRIDGE \ JRNL TITL 2 FACILITATE RATCHET-LIKE MOTION OF THE RIBOSOME \ JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 399 192 2010 \ JRNL REFN ISSN 0006-291X \ JRNL PMID 20643101 \ JRNL DOI 10.1016/J.BBRC.2010.07.053 \ REMARK 2 \ REMARK 2 RESOLUTION. 9.00 ANGSTROMS. \ REMARK 3 \ REMARK 3 REFINEMENT. \ REMARK 3 SOFTWARE PACKAGES : SPIDER \ REMARK 3 RECONSTRUCTION SCHEMA : NULL \ REMARK 3 \ REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT \ REMARK 3 PDB ENTRY : 2I2P \ REMARK 3 REFINEMENT SPACE : NULL \ REMARK 3 REFINEMENT PROTOCOL : NULL \ REMARK 3 REFINEMENT TARGET : NULL \ REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL \ REMARK 3 \ REMARK 3 FITTING PROCEDURE : NULL \ REMARK 3 \ REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS \ REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : 2.820 \ REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL \ REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 9.000 \ REMARK 3 NUMBER OF PARTICLES : 52181 \ REMARK 3 CTF CORRECTION METHOD : NULL \ REMARK 3 \ REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: TMV \ REMARK 3 \ REMARK 3 OTHER DETAILS: NULL \ REMARK 4 \ REMARK 4 3IYX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 \ REMARK 100 \ REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-AUG-10. \ REMARK 100 THE DEPOSITION ID IS D_1000160039. \ REMARK 245 \ REMARK 245 EXPERIMENTAL DETAILS \ REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE \ REMARK 245 SPECIMEN TYPE : VITREOUS ICE (CRYO EM) \ REMARK 245 \ REMARK 245 ELECTRON MICROSCOPE SAMPLE \ REMARK 245 SAMPLE TYPE : PARTICLE \ REMARK 245 PARTICLE TYPE : POINT \ REMARK 245 NAME OF SAMPLE : E.COLI 70S RIBOSOME \ REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL \ REMARK 245 SAMPLE SUPPORT DETAILS : QUANTIFOIL HOLLEY CARBON FILM \ REMARK 245 GRIDS \ REMARK 245 SAMPLE VITRIFICATION DETAILS : RAPID-FREEZING IN LIQUID ETHANE \ REMARK 245 SAMPLE BUFFER : POLYMIX BUFFER \ REMARK 245 PH : 7.50 \ REMARK 245 SAMPLE DETAILS : NULL \ REMARK 245 \ REMARK 245 DATA ACQUISITION \ REMARK 245 DATE OF EXPERIMENT : NULL \ REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL \ REMARK 245 TEMPERATURE (KELVIN) : 93.00 \ REMARK 245 MICROSCOPE MODEL : FEI TECNAI F20 \ REMARK 245 DETECTOR TYPE : KODAK SO-163 FILM \ REMARK 245 MINIMUM DEFOCUS (NM) : 2000.00 \ REMARK 245 MAXIMUM DEFOCUS (NM) : 4000.00 \ REMARK 245 MINIMUM TILT ANGLE (DEGREES) : 0.00 \ REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : 0.00 \ REMARK 245 NOMINAL CS : 2.00 \ REMARK 245 IMAGING MODE : BRIGHT FIELD \ REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 2000.00 \ REMARK 245 ILLUMINATION MODE : FLOOD BEAM \ REMARK 245 NOMINAL MAGNIFICATION : 50000 \ REMARK 245 CALIBRATED MAGNIFICATION : 49696 \ REMARK 245 SOURCE : FIELD EMISSION GUN \ REMARK 245 ACCELERATION VOLTAGE (KV) : 200 \ REMARK 245 IMAGING DETAILS : NULL \ REMARK 247 \ REMARK 247 ELECTRON MICROSCOPY \ REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON \ REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE \ REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES \ REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION \ REMARK 247 OF THE STRUCTURE FACTORS. \ REMARK 300 \ REMARK 300 BIOMOLECULE: 1 \ 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: TRIMERIC \ REMARK 350 APPLY THE FOLLOWING TO CHAINS: M, F, 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 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 M 0 \ REMARK 465 ILE M 115 \ REMARK 465 LYS M 116 \ REMARK 465 LYS M 117 \ REMARK 465 MET F 0 \ REMARK 900 \ REMARK 900 RELATED ENTRIES \ REMARK 900 RELATED ID: 2I2P RELATED DB: PDB \ REMARK 900 CRYSTAL STRUCTURE OF 30S SUBUNIT OF E. COLI RIBOSOME WITH MESSENGER \ REMARK 900 RNA AND THE ANTICODON STEM-LOOP OF P-SITE TRNA. CHAIN M: SMALL \ REMARK 900 SUBUNIT PROTEIN S13 \ REMARK 900 RELATED ID: 2I2T RELATED DB: PDB \ REMARK 900 CRYSTAL STRUCTURE OF 50S SUBUNIT OF E. COLI RIBOSOME WITH MESSENGER \ REMARK 900 RNA AND THE ANTICODON STEM-LOOP OF P-SITE TRNA. CHAIN F: LARGE \ REMARK 900 SUBUNIT PROTEIN L5 \ REMARK 900 RELATED ID: 2WRJ RELATED DB: PDB \ REMARK 900 X-RAY STRUCTURE OF THE T. THERMOPHILUS 70S RIBOSOME (CHAIN 4 WAS \ REMARK 900 USED AS TEMPLATE TO BUILD HOMOLOGY MODEL OF E.COLI L31) \ REMARK 900 RELATED ID: EMD-1056 RELATED DB: EMDB \ REMARK 900 CRYO-EM MAP OF E. COLI 70S-TRNAFMET-MF-TRNAPHE COMPLEX \ DBREF 3IYX M 0 117 UNP D3QTD7 D3QTD7_ECOCB 1 118 \ DBREF 3IYX F 0 178 UNP D3QTE7 D3QTE7_ECOCB 1 179 \ DBREF 3IYX A 1 70 UNP D3QYD6 D3QYD6_ECOCB 1 70 \ SEQRES 1 M 118 MET ALA ARG ILE ALA GLY ILE ASN ILE PRO ASP HIS LYS \ SEQRES 2 M 118 HIS ALA VAL ILE ALA LEU THR SER ILE TYR GLY VAL GLY \ SEQRES 3 M 118 LYS THR ARG SER LYS ALA ILE LEU ALA ALA ALA GLY ILE \ SEQRES 4 M 118 ALA GLU ASP VAL LYS ILE SER GLU LEU SER GLU GLY GLN \ SEQRES 5 M 118 ILE ASP THR LEU ARG ASP GLU VAL ALA LYS PHE VAL VAL \ SEQRES 6 M 118 GLU GLY ASP LEU ARG ARG GLU ILE SER MET SER ILE LYS \ SEQRES 7 M 118 ARG LEU MET ASP LEU GLY CYS TYR ARG GLY LEU ARG HIS \ SEQRES 8 M 118 ARG ARG GLY LEU PRO VAL ARG GLY GLN ARG THR LYS THR \ SEQRES 9 M 118 ASN ALA ARG THR ARG LYS GLY PRO ARG LYS PRO ILE LYS \ SEQRES 10 M 118 LYS \ SEQRES 1 F 179 MET ALA LYS LEU HIS ASP TYR TYR LYS ASP GLU VAL VAL \ SEQRES 2 F 179 LYS LYS LEU MET THR GLU PHE ASN TYR ASN SER VAL MET \ SEQRES 3 F 179 GLN VAL PRO ARG VAL GLU LYS ILE THR LEU ASN MET GLY \ SEQRES 4 F 179 VAL GLY GLU ALA ILE ALA ASP LYS LYS LEU LEU ASP ASN \ SEQRES 5 F 179 ALA ALA ALA ASP LEU ALA ALA ILE SER GLY GLN LYS PRO \ SEQRES 6 F 179 LEU ILE THR LYS ALA ARG LYS SER VAL ALA GLY PHE LYS \ SEQRES 7 F 179 ILE ARG GLN GLY TYR PRO ILE GLY CYS LYS VAL THR LEU \ SEQRES 8 F 179 ARG GLY GLU ARG MET TRP GLU PHE PHE GLU ARG LEU ILE \ SEQRES 9 F 179 THR ILE ALA VAL PRO ARG ILE ARG ASP PHE ARG GLY LEU \ SEQRES 10 F 179 SER ALA LYS SER PHE ASP GLY ARG GLY ASN TYR SER MET \ SEQRES 11 F 179 GLY VAL ARG GLU GLN ILE ILE PHE PRO GLU ILE ASP TYR \ SEQRES 12 F 179 ASP LYS VAL ASP ARG VAL ARG GLY LEU ASP ILE THR ILE \ SEQRES 13 F 179 THR THR THR ALA LYS SER ASP GLU GLU GLY ARG ALA LEU \ SEQRES 14 F 179 LEU ALA ALA PHE ASP PHE PRO PHE ARG LYS \ SEQRES 1 A 70 MET LYS LYS ASP ILE HIS PRO LYS TYR GLU GLU ILE THR \ SEQRES 2 A 70 ALA SER CYS SER CYS GLY ASN VAL MET LYS ILE ARG SER \ SEQRES 3 A 70 THR VAL GLY HIS ASP LEU ASN LEU ASP VAL CYS SER LYS \ SEQRES 4 A 70 CYS HIS PRO PHE PHE THR GLY LYS GLN ARG ASP VAL ALA \ SEQRES 5 A 70 THR GLY GLY ARG VAL ASP ARG PHE ASN LYS ARG PHE ASN \ SEQRES 6 A 70 ILE PRO GLY SER LYS \ CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 1 \ 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 1.000000 0.000000 0.000000 0.00000 \ SCALE2 0.000000 1.000000 0.000000 0.00000 \ SCALE3 0.000000 0.000000 1.000000 0.00000 \ TER 115 PRO M 114 \ TER 294 LYS F 178 \ ATOM 295 CA MET A 1 -57.085 -73.159 -9.981 0.00 0.00 C \ ATOM 296 CA LYS A 2 -53.896 -74.388 -8.098 0.00 0.00 C \ ATOM 297 CA LYS A 3 -51.627 -72.816 -5.324 1.00 0.00 C \ ATOM 298 CA ASP A 4 -54.494 -73.333 -2.710 1.00 0.00 C \ ATOM 299 CA ILE A 5 -55.856 -69.673 -2.571 0.00 0.00 C \ ATOM 300 CA HIS A 6 -59.003 -70.129 -4.820 0.00 0.00 C \ ATOM 301 CA PRO A 7 -62.756 -70.521 -3.747 0.00 0.00 C \ ATOM 302 CA LYS A 8 -62.535 -74.450 -3.942 0.00 0.00 C \ ATOM 303 CA TYR A 9 -65.070 -74.765 -6.905 1.00 0.00 C \ ATOM 304 CA GLU A 10 -68.143 -76.662 -5.477 1.00 0.00 C \ ATOM 305 CA GLU A 11 -71.196 -78.326 -7.222 1.00 0.00 C \ ATOM 306 CA ILE A 12 -74.422 -76.238 -7.534 1.00 0.00 C \ ATOM 307 CA THR A 13 -78.183 -76.126 -8.423 1.00 0.00 C \ ATOM 308 CA ALA A 14 -80.098 -73.011 -9.688 1.00 0.00 C \ ATOM 309 CA SER A 15 -83.531 -72.659 -7.895 1.00 0.00 C \ ATOM 310 CA CYS A 16 -85.393 -70.972 -10.796 0.00 0.00 C \ ATOM 311 CA SER A 17 -88.871 -70.231 -9.234 1.00 0.00 C \ ATOM 312 CA CYS A 18 -90.493 -71.260 -12.590 0.00 0.00 C \ ATOM 313 CA GLY A 19 -89.309 -74.948 -12.535 0.00 0.00 C \ ATOM 314 CA ASN A 20 -86.180 -74.959 -14.837 0.00 0.00 C \ ATOM 315 CA VAL A 21 -83.337 -75.929 -12.358 0.00 0.00 C \ ATOM 316 CA MET A 22 -79.819 -75.833 -13.958 1.00 0.00 C \ ATOM 317 CA LYS A 23 -77.293 -78.257 -12.253 1.00 0.00 C \ ATOM 318 CA ILE A 24 -73.824 -76.504 -12.630 1.00 0.00 C \ ATOM 319 CA ARG A 25 -70.639 -75.625 -10.545 1.00 0.00 C \ ATOM 320 CA SER A 26 -68.605 -72.678 -8.894 0.00 0.00 C \ ATOM 321 CA THR A 27 -69.189 -71.079 -5.348 0.00 0.00 C \ ATOM 322 CA VAL A 28 -71.680 -69.534 -2.770 1.00 0.00 C \ ATOM 323 CA GLY A 29 -74.318 -71.939 -4.189 1.00 0.00 C \ ATOM 324 CA HIS A 30 -75.683 -74.788 -3.709 1.00 0.00 C \ ATOM 325 CA ASP A 31 -78.701 -72.439 -3.126 1.00 0.00 C \ ATOM 326 CA LEU A 32 -78.742 -70.002 -6.167 1.00 0.00 C \ ATOM 327 CA ASN A 33 -82.341 -68.540 -6.605 1.00 0.00 C \ ATOM 328 CA LEU A 34 -84.123 -66.784 -9.591 1.00 0.00 C \ ATOM 329 CA ASP A 35 -87.492 -64.971 -10.278 1.00 0.00 C \ ATOM 330 CA VAL A 36 -90.523 -65.089 -12.724 1.00 0.00 C \ ATOM 331 CA CYS A 37 -91.426 -61.779 -14.559 1.00 0.00 C \ ATOM 332 CA SER A 38 -87.732 -60.740 -14.867 1.00 0.00 C \ ATOM 333 CA LYS A 39 -84.711 -60.634 -17.314 1.00 0.00 C \ ATOM 334 CA CYS A 40 -81.881 -63.198 -18.281 1.00 0.00 C \ ATOM 335 CA HIS A 41 -83.482 -66.730 -18.500 1.00 0.00 C \ ATOM 336 CA PRO A 42 -82.954 -68.749 -21.790 1.00 0.00 C \ ATOM 337 CA PHE A 43 -86.730 -69.647 -21.633 1.00 0.00 C \ ATOM 338 CA PHE A 44 -87.826 -65.908 -21.387 1.00 0.00 C \ ATOM 339 CA THR A 45 -89.460 -63.572 -24.033 1.00 0.00 C \ ATOM 340 CA GLY A 46 -86.018 -62.298 -25.325 1.00 0.00 C \ ATOM 341 CA LYS A 47 -87.206 -60.660 -28.629 1.00 0.00 C \ ATOM 342 CA GLN A 48 -87.130 -57.324 -30.589 1.00 0.00 C \ ATOM 343 CA ARG A 49 -89.265 -54.145 -29.950 1.00 0.00 C \ ATOM 344 CA ASP A 50 -90.467 -51.005 -31.900 1.00 0.00 C \ ATOM 345 CA VAL A 51 -89.445 -47.227 -32.014 1.00 0.00 C \ ATOM 346 CA ALA A 52 -91.649 -43.998 -32.267 1.00 0.00 C \ ATOM 347 CA THR A 53 -93.366 -41.614 -34.815 1.00 0.00 C \ ATOM 348 CA GLY A 54 -95.216 -38.206 -34.459 1.00 0.00 C \ ATOM 349 CA GLY A 55 -94.797 -34.488 -35.550 1.00 0.00 C \ ATOM 350 CA ARG A 56 -97.430 -32.328 -33.655 1.00 0.00 C \ ATOM 351 CA VAL A 57 -96.197 -28.697 -34.316 1.00 0.00 C \ ATOM 352 CA ASP A 58 -98.697 -26.575 -36.404 1.00 0.00 C \ ATOM 353 CA ARG A 59 -97.774 -25.300 -39.966 1.00 0.00 C \ ATOM 354 CA PHE A 60 -97.307 -21.581 -38.875 1.00 0.00 C \ ATOM 355 CA ASN A 61 -99.853 -19.786 -41.198 1.00 0.00 C \ ATOM 356 CA LYS A 62 -102.541 -22.435 -40.254 1.00 0.00 C \ ATOM 357 CA ARG A 63 -104.724 -22.295 -43.475 1.00 0.00 C \ ATOM 358 CA PHE A 64 -108.052 -24.303 -43.456 1.00 0.00 C \ ATOM 359 CA ASN A 65 -109.735 -24.059 -39.967 1.00 0.00 C \ ATOM 360 CA ILE A 66 -113.061 -23.372 -38.056 1.00 0.00 C \ ATOM 361 CA PRO A 67 -114.369 -21.203 -35.103 1.00 0.00 C \ ATOM 362 CA GLY A 68 -112.883 -22.399 -31.725 1.00 0.00 C \ ATOM 363 CA SER A 69 -113.497 -20.442 -28.417 1.00 0.00 C \ ATOM 364 CA LYS A 70 -116.025 -22.541 -26.299 1.00 0.00 C \ TER 365 LYS A 70 \ MASTER 120 0 0 0 0 0 0 6 362 3 0 30 \ END \ """, "3iyxchainA") cmd.hide("all") cmd.color('grey70', "3iyxchainA") cmd.show('cartoon', "3iyxchainA") cmd.center("3iyxchainA", state=0, origin=1) cmd.zoom("3iyxchainA", animate=-1) cmd.select("e3iyxA1", "c. 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