2O5R

Crystal structure of Glutamyl-tRNA synthetase 1 (EC 6.1.1.17) (Glutamate-tRNA ligase 1) (GluRS 1) (TM1351) from Thermotoga maritima at 2.5 A resolution

PDB DOI: https://doi.org/10.2210/pdb2O5R/pdb

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

Deposited: 2006-12-06 Released: 2006-12-19
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free: 0.268
R-Value Work: 0.234
R-Value Observed: 0.236

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.8 of the entry. See complete history.

Literature

Crystal structure of Glutamyl-tRNA synthetase 1 (EC 6.1.1.17) (Glutamate-tRNA ligase 1) (GluRS 1) (TM1351) from Thermotoga maritima at 2.5 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 57.05 kDa
Atom Count: 3,897
Modelled Residue Count: 468
Deposited Residue Count: 481
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamyl-tRNA synthetase 1	A	481	Thermotoga maritima	Mutation(s): 14 Gene Names: gltX1 EC: 6.1.1.17
UniProt
Find proteins for Q9X172 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X172 Go to UniProtKB: Q9X172
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9X172
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free: 0.268
R-Value Work: 0.234
R-Value Observed: 0.236
Space Group: P 3₁ 2 1
Diffraction Data: https://doi.org/10.18430/M32O5R

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.953	α = 90
b = 69.953	β = 90
c = 283.945	γ = 120

Software Package:

Software Name	Purpose
SHELX	phasing
SOLVE	phasing
MOLREP	phasing
RESOLVE	phasing
REFMAC	refinement
XSCALE	data scaling
MolProbity	model building
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2006-12-19

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2006-12-19
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2017-10-25
Changes: Author supporting evidence
Version 1.5: 2023-01-25
Changes: Database references, Derived calculations
Version 1.6: 2023-09-20
Changes: Data collection, Refinement description
Version 1.7: 2023-11-15
Changes: Data collection
Version 1.8: 2024-10-30
Changes: 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.