2CX3

Crystal structure of a bacterioferritin comigratory protein peroxiredoxin from the Aeropyrum pernix K1 (form-1 crystal)

• PDB DOI: https://doi.org/10.2210/pdb2CX3/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aeropyrum pernix K1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-06-27 Released: 2005-12-27 
• Deposition Author(s): Mizohata, E., Murayama, K., Idaka, M., Tatsuguchi, A., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 0.247 
• R-Value Work: 0.206 
• R-Value Observed: 0.206 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 4GQF

Literature

Crystal structure of a bacterioferritin comigratory protein peroxiredoxin from the Aeropyrum pernix K1 (form-1 crystal)

Mizohata, E., Murayama, K., Idaka, M., Tatsuguchi, A., Terada, T., Shirouzu, M., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 75.34 kDa 
• Atom Count: 5,360 
• Modelled Residue Count: 641 
• Deposited Residue Count: 656 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
bacterioferritin comigratory protein	A, B, C, D	164	Aeropyrum pernix K1	Mutation(s): 3  Gene Names: APE2125 EC: 1.11.1.15
UniProt
Find proteins for Q9YA14 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9YA14  Go to UniProtKB:  Q9YA14

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 0.247 
• R-Value Work: 0.206 
• R-Value Observed: 0.206 
• Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.99	α = 90
b = 126.99	β = 90
c = 104.856	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-27 
Deposition Author(s): Mizohata, E., Murayama, K., Idaka, M., Tatsuguchi, A., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2005-12-27
  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
• Version 1.3: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary