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)

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

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of Glutamate-tRNA Synthetase from Helicobacter pylori

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

To be published.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B5Z6J9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-09-27

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.