3DQQ | pdb_00003dqq

The crystal structure of the putative tRNA synthase from Salmonella typhimurium LT2

PDB DOI: https://doi.org/10.2210/pdb3DQQ/pdb

Classification: structural genomics, unknown function
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-07-09 Released: 2008-07-22
Deposition Author(s): Zhang, R., Gu, M., Zhou, M., Anderson, W., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.210 (Depositor), 0.215 (DCC)
R-Value Work:
0.188 (Depositor), 0.194 (DCC)
R-Value Observed:
0.189 (Depositor)

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

Literature

The crystal structure of the putative tRNA synthase from Salmonella typhimurium LT2

Zhang, R., Gu, M., Zhou, M., Anderson, W., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 89.77 kDa
Atom Count: 6,264
Modeled Residue Count: 831
Deposited Residue Count: 842
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative tRNA synthase	A, B	421	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0 Gene Names: ygbK, STM2917 EC: 2.7.1.217
UniProt
Find proteins for Q8ZMG5 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZMG5 Go to UniProtKB: Q8ZMG5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8ZMG5
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.210 (Depositor), 0.215 (DCC)
R-Value Work: 0.188 (Depositor), 0.194 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 254.541	α = 90
b = 254.541	β = 90
c = 94.459	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-07-22

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2008-07-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations

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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.