1J5W | pdb_00001j5w

Crystal structure of Glycyl-tRNA synthetase alpha chain (TM0216) from Thermotoga maritima at 1.95 A resolution

PDB DOI: https://doi.org/10.2210/pdb1J5W/pdb

Classification: LIGASE
Organism(s): Thermotoga maritima
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2002-07-05 Released: 2002-07-17
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.254 (Depositor), 0.260 (DCC)
R-Value Work:
0.197 (Depositor), 0.210 (DCC)
R-Value Observed:
0.197 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of Glycyl-tRNA synthetase alpha chain (TM0216) from Thermotoga maritima at 1.95 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 70.73 kDa
Atom Count: 4,829
Modeled Residue Count: 554
Deposited Residue Count: 596
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycyl-tRNA synthetase alpha chain	A, B	298	Thermotoga maritima	Mutation(s): 6 Gene Names: TM0216 EC: 6.1.1.14
UniProt
Find proteins for Q9WY59 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WY59 Go to UniProtKB: Q9WY59
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9WY59
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.254 (Depositor), 0.260 (DCC)
R-Value Work: 0.197 (Depositor), 0.210 (DCC)
R-Value Observed: 0.197 (Depositor)

Diffraction Data: https://doi.org/10.18430/M31J5W

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.4	α = 90
b = 66.2	β = 90
c = 142.1	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
CCP4	data reduction
SOLVE	phasing
RESOLVE	model building
CNS	refinement
CCP4	data scaling
RESOLVE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2002-07-17

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2002-07-17
Type: Initial release
Version 1.1: 2008-04-26
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2018-07-18
Changes: Data collection, Database references
Version 1.4: 2023-01-25
Changes: Database references, Derived calculations
Version 1.5: 2024-11-20
Changes: Data collection, Structure summary

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.