1WDV

Crystal structure of hypothetical protein APE2540

• PDB DOI: https://doi.org/10.2210/pdb1WDV/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Aeropyrum pernix K1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-05-18 Released: 2004-11-18 
• Deposition Author(s): Murayama, K., Kato-Murayama, M., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.206 
• R-Value Work: 0.169 
• R-Value Observed: 0.169 

Literature

Structure of a putative trans-editing enzyme for prolyl-tRNA synthetase from Aeropyrum pernix K1 at 1.7 A resolution.

Murayama, K., Kato-Murayama, M., Katsura, K., Uchikubo-Kamo, T., Yamaguchi-Hirafuji, M., Kawazoe, M., Akasaka, R., Hanawa-Suetsugu, K., Hori-Takemoto, C., Terada, T., Shirouzu, M., Yokoyama, S.

(2005) Acta Crystallogr Sect F Struct Biol Cryst Commun 61: 26-29

• PubMed: 16508081 
• DOI: https://doi.org/10.1107/S1744309104032555
• Primary Citation of Related Structures:  
  1WDV


• PubMed Abstract: 
  

  The crystal structure of APE2540, the putative trans-editing enzyme ProX from Aeropyrum pernix K1, was determined in a high-throughput manner. The crystal belongs to the monoclinic space group P2(1), with unit-cell parameters a = 47.4, b = 58.9, c = 53.6 A, beta = 106.8 degrees. The structure was solved by the multiwavelength anomalous dispersion method at 1.7 A and refined to an R factor of 16.8% (Rfree = 20.5%). The crystal structure includes two protein molecules in the asymmetric unit. Each monomer consists of eight beta-strands and seven alpha-helices. A structure-homology search revealed similarity between the trans-editing enzyme YbaK (or cysteinyl-tRNAPro deacylase) from Haemophilus influenzae (HI1434; 22% sequence identity) and putative ProX proteins from Caulobacter crescentus (16%) and Agrobacterium tumefaciens (21%).

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Organizational Affiliation: 

RIKEN Genomic Sciences Center, Yokohama, 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.

Macromolecule Content

• Total Structure Weight: 32.96 kDa 
• Atom Count: 2,767 
• Modelled Residue Count: 300 
• Deposited Residue Count: 304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein APE2540	A, B	152	Aeropyrum pernix K1	Mutation(s): 3
UniProt
Find proteins for Q9Y8U3 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9Y8U3  Go to UniProtKB:  Q9Y8U3

Small Molecules

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: 1.70 Å
• R-Value Free: 0.206 
• R-Value Work: 0.169 
• R-Value Observed: 0.169 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.435	α = 90
b = 58.917	β = 106.8
c = 53.603	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-11-18 
Deposition Author(s): Murayama, K., Kato-Murayama, M., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2004-11-18
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance