5H4V

Structure of glutamyl-tRNA synthetase (Xoo1504) from Xanthomonas oryzae pv. oryzae

PDB DOI: https://doi.org/10.2210/pdb5H4V/pdb

Classification: LIGASE
Organism(s): Xanthomonas oryzae pv. oryzae KACC 10331
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2016-11-02 Released: 2017-10-11
Deposition Author(s): Doan, T.-N.-T., Ho, T.-H., Kang, L.-W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.291
R-Value Work: 0.200
R-Value Observed: 0.204

wwPDB Validation 3D Report Full Report

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

Literature

Transcriptional expression of aminoacyl tRNA synthetase genes of Xanthomonas oryzae pv. oryzae (Xoo) on rice-leaf extract treatment and crystal structure of Xoo glutamyl-tRNA synthetase

Ho, T.-H., Hong, M.-K., Kim, S., Kim, J.-G., Lee, J., Jung, K., Lee, I., Choi, M., Park, H., Lee, S., Ahn, Y.-J., Kang, L.-W.

(2017) Crop Pasture Sci 68: 434-441

DOI: https://doi.org/10.1071/CP16435

Macromolecule Content

Total Structure Weight: 325.09 kDa
Atom Count: 21,668
Modelled Residue Count: 2,775
Deposited Residue Count: 2,928
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	A, B, C, D, E A, B, C, D, E, F	488	Xanthomonas oryzae pv. oryzae KACC 10331	Mutation(s): 0 Gene Names: gltX, XOO1504 EC: 6.1.1.17
UniProt
Find proteins for Q5H2R3 (Xanthomonas oryzae pv. oryzae (strain KACC10331 / KXO85)) Explore Q5H2R3 Go to UniProtKB: Q5H2R3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5H2R3
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.291
R-Value Work: 0.200
R-Value Observed: 0.204
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 186.353	α = 90
b = 107.937	β = 96.24
c = 165.895	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-10-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-10-11
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Refinement description

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 R01GM133198.