6B1P | pdb_00006b1p

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 (Depositor), 0.277 (DCC)
R-Value Work:
0.234 (Depositor), 0.233 (DCC)
R-Value Observed:
0.239 (Depositor)

Starting Model: experimental
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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
Modeled Residue Count: 430
Deposited Residue Count: 471
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF 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 (Depositor), 0.277 (DCC)
R-Value Work: 0.234 (Depositor), 0.233 (DCC)
R-Value Observed: 0.239 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

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

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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

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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.