2YWB | pdb_00002ywb

Crystal structure of GMP synthetase from Thermus thermophilus

PDB DOI: https://doi.org/10.2210/pdb2YWB/pdb

Classification: LIGASE
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-04-20 Released: 2007-10-23
Deposition Author(s): Baba, S., Kanagawa, M., Yanai, H., Ishii, T., Kuramitsu, S., Yokoyama, S., Sampei, G., Kawai, G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.272 (Depositor), 0.241 (DCC)
R-Value Work:
0.233 (Depositor), 0.243 (DCC)
R-Value Observed:
0.233 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of GMP synthetase from Thermus thermophilus

Baba, S., Kanagawa, M., Yanai, H., Ishii, T., Kuramitsu, S., Yokoyama, S., Sampei, G., Kawai, G.

To be published.

Macromolecule Content

Total Structure Weight: 223.58 kDa
Atom Count: 15,065
Modeled Residue Count: 1,863
Deposited Residue Count: 2,012
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GMP synthase [glutamine-hydrolyzing]	A, B, C, D	503	Thermus thermophilus HB8	Mutation(s): 0 Gene Names: guaA EC: 6.3.5.2
UniProt
Find proteins for Q5SI28 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SI28 Go to UniProtKB: Q5SI28
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SI28
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.272 (Depositor), 0.241 (DCC)
R-Value Work: 0.233 (Depositor), 0.243 (DCC)
R-Value Observed: 0.233 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.949	α = 90
b = 114.854	β = 93.37
c = 160.033	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-10-23

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2007-10-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Derived calculations, Source and taxonomy, Version format compliance
Version 1.2: 2024-03-13
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.