5H4V | pdb_00005h4v

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 (Depositor), 0.289 (DCC)
R-Value Work:
0.200 (Depositor), 0.206 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
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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
Modeled Residue Count: 2,775
Deposited Residue Count: 2,928
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 (Depositor), 0.289 (DCC)
R-Value Work: 0.200 (Depositor), 0.206 (DCC)
R-Value Observed: 0.204 (Depositor)

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

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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

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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.