1WE0 | pdb_00001we0

Crystal structure of peroxiredoxin (AhpC) from Amphibacillus xylanus

• PDB DOI: https://doi.org/10.2210/pdb1WE0/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Amphibacillus xylanus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-05-21 Released: 2005-03-29 
• Deposition Author(s): Kitano, K., Kita, A., Hakoshima, T., Niimura, Y., Miki, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.235 (Depositor) 
• R-Value Work: 
  0.208 (Depositor) 

Literature

Crystal structure of decameric peroxiredoxin (AhpC) from Amphibacillus xylanus

Kitano, K., Kita, A., Hakoshima, T., Niimura, Y., Miki, K.

(2005) Proteins 59: 644-647

• PubMed: 15770647 
• DOI: https://doi.org/10.1002/prot.20412
• Primary Citation Related Structures: 
  1WE0

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Organizational Affiliation: 
• Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan.

Biological Assembly 1  

Global Symmetry: Dihedral - D5  (Explore in 3D)
Global Stoichiometry: Homo 10-mer - A10 

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

Macromolecule Content 

• Total Structure Weight: 206.67 kDa 
• Atom Count: 12,982 
• Modeled Residue Count: 1,660 
• Deposited Residue Count: 1,870 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
alkyl hydroperoxide reductase C	A, B, C, D, E, F, G, H, I, J	187	Amphibacillus xylanus	Mutation(s): 0  EC: 1.11.1 (PDB Primary Data), 1.11.1.26 (UniProt)
UniProt
Find proteins for K0J4Q8 (Amphibacillus xylanus (strain ATCC 51415 / DSM 6626 / JCM 7361 / LMG 17667 / NBRC 15112 / Ep01)) Explore K0J4Q8  Go to UniProtKB:  K0J4Q8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NH4	K [auth F], L [auth J]	AMMONIUM ION H4 N QGZKDVFQNNGYKY-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.235 (Depositor) 
• R-Value Work:  0.208 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.216	α = 77.22
b = 79.319	β = 82.33
c = 104.449	γ = 80.08

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-29 
Deposition Author(s): Kitano, K., Kita, A., Hakoshima, T., Niimura, Y., Miki, K.

Revision History  

• Version 1.0: 2005-03-29
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2018-02-07
  Changes: Experimental preparation
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary