2O5R | pdb_00002o5r

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 (Depositor), 0.276 (DCC)
R-Value Work:
0.234 (Depositor), 0.239 (DCC)
R-Value Observed:
0.236 (Depositor)

Starting Model: experimental
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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
Modeled Residue Count: 468
Deposited Residue Count: 481
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [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 (Depositor), 0.276 (DCC)
R-Value Work: 0.234 (Depositor), 0.239 (DCC)
R-Value Observed: 0.236 (Depositor)

Diffraction Data:

Space Group: P 3₁ 2 1

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

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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

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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.