3RF1 | pdb_00003rf1

The crystal structure of glycyl-tRNA synthetase subunit alpha from Campylobacter jejuni subsp. jejuni NCTC 11168

• PDB DOI: https://doi.org/10.2210/pdb3RF1/pdb

• Classification: LIGASE
• Organism(s): Campylobacter jejuni subsp. jejuni 81-176
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-04-05 Released: 2011-04-20 
• Deposition Author(s): Tan, K., Zhang, R., Zhou, M., Hasseman, J., 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: 2.20 Å
• R-Value Free: 
  0.214 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of glycyl-tRNA synthetase subunit alpha from Campylobacter jejuni subsp. jejuni NCTC 11168

Tan, K., Zhang, R., Zhou, M., Hasseman, J., 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: 73.24 kDa 
• Atom Count: 4,783 
• Modeled Residue Count: 577 
• 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 subsp. jejuni 81-176	Mutation(s): 0  Gene Names: glyQ, CJJ81176_0727 EC: 6.1.1.14
UniProt
Find proteins for A1VZ59 (Campylobacter jejuni subsp. jejuni serotype O:23/36 (strain 81-176)) Explore A1VZ59  Go to UniProtKB:  A1VZ59

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LMR	C [auth A], E [auth B]	(2S)-2-hydroxybutanedioic acid C4 H6 O5 BJEPYKJPYRNKOW-REOHCLBHSA-N
GOL	D [auth A], F [auth B], G [auth B], H [auth B], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 2.20 Å
• R-Value Free:  0.214 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33rf1

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.662	α = 90
b = 112.662	β = 90
c = 158.282	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: 2011-04-20 
Deposition Author(s): Tan, K., Zhang, R., Zhou, M., Hasseman, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-04-20
  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: 2024-11-27
  Changes: Structure summary