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T0589

© 2010 Grishin lab/HHMI/UTSW

updated on 2010-12-20

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643

T0589

3NET from Nostoc sp. PCC 7120

Target sequence:

>T0589 3NET, Nostoc sp. PCC 7120, 465 residues
SNAMAKNDKINFSTPSGFPEFLPSEKRLELYLLDTIRRVYESYGFTPIETPAVERLEVLQAKGNQGDNIIYGLEPILPPNRQAEKDKSGDTGSEARALKFDQTVPLAAYIARHLNDLTFPFARYQMDVVFRGERAKDGRFRQFRQCDIDVVGREKLSLLYDAQMPAIITEIFEAVNIGDFVIRINNRKVLTGFFQSLNISETQIKSCISIIDNLEKIGEAKVKLELEKEGINPEQTQKIIDFVKIDGSVDDVLDKLKHLSQTLPESEQFNLGVSELETVITGVRNLGVPDKRFCIDLAIARGLNYYTGTVYETTLIGHEALGSICSGGRYEELVGTFIGEKMPGVGISIGLTRLISRLLKAGILNTLPPTPAQVVVVNMQDELMPTYLKVSQQLRQAGLNVITNFEKRQLGKQFQAADKQGIRFCVIIGADEAAAQKSSLKDLQSGEQVEVALADLAEEIKRRLT

HHsearch_pdb70_15May10,  HHsearch_scop70_1.75,  HHsearch_pfamA.24.0, HorAServer, HorAServer (T0589d1+2), HorAServer (T0589d3), Dali Result

Structure:

Method: X-ray, res= Å, R/Rfree=

Determined by: MCSG

PDB ID: 3net

Domains:   PyMOL of domains

Three domains.

To compute the weighted sum, GDT-TS for each domain was multiplied by the domain length, and this sum was divided by the sum of domain lengths. Each point represents first server model. Green, gray and black points are top 10, bottom 25% and the rest of prediction models. Blue line is the best-fit slope line (intersection 0) to the top 10 server models. Red line is the diagonal. Slope and root mean square y-x distance for the top 10 models (average difference between the weighted sum of domain GDT-TS scores and the whole chain GDT-TS score) are shown above the plot.

Structure classification:

The description below was written months before target structure release, thus it only presents shuoyong's personal thoughts simply based on sequence. Please be aware that it may contain laughable errors. It is certainly not our final assessment on this target. We will revise this section (and the sequence classification too) in a short time

Histidyl-tRNA synthetas. Two domain proteins. N-terminal (around 9-364) is a Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain, C-terminal (around 365-end) is a Anticodon-binding domain of Class II aaRS.

CASP category:

T0589 needs domain-based evaluation, and domain 1 and domain 2 needs to be merged as a evaluation unit

1st domain: TBM  alignment. 2rd domain: TBM  alignment. 3th domain: TBM  alignment. Combined domain (domain 1 merged with domain 2): TBM  alignment.

Closest templates:

Template manually selected by shuoyong:

3lc0_A | PyMOL of 3lc0 A

  

Template selected by HHpred server group:

• 3lc0_A | PyMOL

• 1wu7_A | PyMOL | this pdbchain contains scop domain: d1wu7a1 A:330-426, d1wu7a2 A:3-329

• 1htt_A | PyMOL | this pdbchain contains scop domain: d1htta1 A:326-424, d1htta2 A:4-325

• 1z7m_A | PyMOL | this pdbchain contains scop domain: d1z7ma1 A:6-323

• 1v95_A | PyMOL | this pdbchain contains scop domain: d1v95a_ A:

Target sequence - PDB file inconsistencies:

Sequence classification:

N-terminal: tRNA synthetase class II core domain (PF00587, C-terminal: Anticodon binding domain (PF03129).

All predictions:

TS (GDT_TS score), TR (GDT_TS with penalty [reference]

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