3RGL | pdb_00003rgl

The crystal structure of glycyl-tRNA synthetase subunit alpha from Campylobacter jejuni subsp. jejuni NCTC in complex with ATP and glycine

• PDB DOI: https://doi.org/10.2210/pdb3RGL/pdb

• Classification: LIGASE
• Organism(s): Campylobacter jejuni
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-04-08 Released: 2011-06-08 
• Deposition Author(s): Tan, K., Zhang, R., Zhou, M., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.233 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of glycyl-tRNA synthetase subunit alpha from Campylobacter jejuni subsp. jejuni NCTC in complex with ATP and glycine.

Tan, K., Zhang, R., Zhou, M., Kwon, K., Anderson, W.F., Joachimiak, A.

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)

Macromolecule Content 

• Total Structure Weight: 73.73 kDa 
• Atom Count: 4,787 
• Modeled Residue Count: 578 
• Deposited Residue Count: 622 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycyl-tRNA synthetase alpha subunit	A, B	311	Campylobacter jejuni	Mutation(s): 0  Gene Names: Cj0704, glyQ EC: 6.1.1.14
UniProt
Find proteins for Q9PPK3 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)) Explore Q9PPK3  Go to UniProtKB:  Q9PPK3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	D [auth A], E [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
LMR	F [auth B]	(2S)-2-hydroxybutanedioic acid C4 H6 O5 BJEPYKJPYRNKOW-REOHCLBHSA-N
GLY	C [auth A]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.233 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33rgl

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.74	α = 90
b = 112.74	β = 90
c = 157.753	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
MOLREP	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-08 
Deposition Author(s): Tan, K., Zhang, R., Zhou, M., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-06-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-12-06
  Changes: Data collection
• Version 1.4: 2024-11-20
  Changes: Structure summary