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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 
  0.268 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

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

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	B [auth A], C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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), 0.280 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32O5R

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

Entry History 

Deposition Data

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

Revision History  

• 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