6B1P

Crystal Structure of Glutamate-tRNA Synthetase from Helicobacter pylori

• PDB DOI: https://doi.org/10.2210/pdb6B1P/pdb

• Classification: LIGASE
• Organism(s): Helicobacter pylori G27
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-09-18 Released: 2017-09-27 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.281 
• R-Value Work: 0.234 
• R-Value Observed: 0.239 

Starting Model: experimental

Literature

Crystal Structure of Glutamate-tRNA Synthetase from Helicobacter pylori

Dranow, D.M., Lorimer, D.D., Edwards, T.E.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 54.48 kDa 
• Atom Count: 3,249 
• Modelled Residue Count: 430 
• Deposited Residue Count: 471 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate--tRNA ligase 1	A	471	Helicobacter pylori G27	Mutation(s): 0  Gene Names: gltX1, HPG27_434 EC: 6.1.1.17
UniProt
Find proteins for B5Z6J9 (Helicobacter pylori (strain G27)) Explore B5Z6J9  Go to UniProtKB:  B5Z6J9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.281 
• R-Value Work: 0.234 
• R-Value Observed: 0.239 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/M36B1P

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 203.05	α = 90
b = 44.6	β = 90
c = 54.12	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MR-Rosetta	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-27 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2017-09-27
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description