7XOF

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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free: 0.250 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 

Starting Model: experimental

Literature

Crystal structure of Oryza sativa plastid glycyl-tRNA synthetase

Hao, Q., Yu, Z., Lu, G., Lin, J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

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

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free: 0.250 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 
• 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

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-24 
Deposition Author(s): Yu, Z., Lu, G., Li, J.

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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  

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