1V4P

Crystal structure of Alanyl-tRNA Synthetase from Pyrococcus horikoshii OT3

• PDB DOI: https://doi.org/10.2210/pdb1V4P/pdb

• Classification: LIGASE
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-11-14 Released: 2004-11-23 
• Deposition Author(s): Ishijima, J., Yutani, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.227 
• R-Value Work: 0.206 
• R-Value Observed: 0.207 

Literature

Crystal structure of alanyl-tRNA synthetase editing-domain homolog (PH0574) from a hyperthermophile, Pyrococcus horikoshii OT3 at 1.45 A resolution

Ishijima, J., Uchida, Y., Kuroishi, C., Tuzuki, C., Takahashi, N., Okazaki, N., Yutani, K., Miyano, M.

(2006) Proteins 62: 1133-1137

• PubMed: 16374837 
• DOI: https://doi.org/10.1002/prot.20760
• Primary Citation of Related Structures:  
  1V4P

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Organizational Affiliation: 

RIKEN SPring-8 Center, Harima Institute, Hyogo, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 54.75 kDa 
• Atom Count: 4,326 
• Modelled Residue Count: 457 
• Deposited Residue Count: 471 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
alanyl-tRNA synthetase	A, B, C	157	Pyrococcus horikoshii	Mutation(s): 0  EC: 6.1.1.7
UniProt
Find proteins for O58307 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58307  Go to UniProtKB:  O58307

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A], E [auth B], F [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.227 
• R-Value Work: 0.206 
• R-Value Observed: 0.207 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.802	α = 90
b = 97.861	β = 96.51
c = 60.872	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-11-23 
Deposition Author(s): Ishijima, J., Yutani, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2004-11-23
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations