7XOF | pdb_00007xof

Crystal structure of Oryza sativa plastid glycyl-tRNA synthetase

PDB DOI: https://doi.org/10.2210/pdb7XOF/pdb

Classification: LIGASE
Organism(s): Oryza sativa Japonica Group
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-05-01 Released: 2023-05-24
Deposition Author(s): Yu, Z., Lu, G., Li, J.
Funding Organization(s): National Natural Science Foundation of China (NSFC), Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.56 Å
R-Value Free:
0.250 (Depositor), 0.250 (DCC)
R-Value Work:
0.210 (Depositor), 0.210 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Oryza sativa plastid glycyl-tRNA synthetase

Hao, Q., Yu, Z., Lu, G., Lin, J.

To be published.

Macromolecule Content

Total Structure Weight: 234.1 kDa
Atom Count: 14,829
Modeled Residue Count: 1,851
Deposited Residue Count: 2,090
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine--tRNA ligase	A, B	1,045	Oryza sativa Japonica Group	Mutation(s): 0 Gene Names: Os06g0103600, OsJ_19814, OSNPB_060103600 EC: 6.1.1.14
UniProt
Find proteins for Q0DFB6 (Oryza sativa subsp. japonica) Explore Q0DFB6 Go to UniProtKB: Q0DFB6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q0DFB6
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.56 Å
R-Value Free: 0.250 (Depositor), 0.250 (DCC)
R-Value Work: 0.210 (Depositor), 0.210 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.13	α = 90
b = 130.94	β = 101.88
c = 123.39	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-05-24

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32130063
National Natural Science Foundation of China (NSFC)	China	31770784
Not funded		2017YFA0504602

Revision History (Full details and data files)

Version 1.0: 2023-05-24
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, 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.