3W6G

Structure of peroxiredoxin from anaerobic hyperthermophilic archaeon Pyrococcus horikoshii

• PDB DOI: https://doi.org/10.2210/pdb3W6G/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-02-14 Released: 2013-07-10 
• Deposition Author(s): Nakamura, T., Mori, A., Niiyama, M., Matsumura, H., Tokuyama, C., Morita, J., Uegaki, K., Inoue, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.237 
• R-Value Work: 0.198 
• R-Value Observed: 0.198 

Literature

Structure of peroxiredoxin from the anaerobic hyperthermophilic archaeon Pyrococcus horikoshii

Nakamura, T., Mori, A., Niiyama, M., Matsumura, H., Tokuyama, C., Morita, J., Uegaki, K., Inoue, T.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 719-722

• PubMed: 23832195 
• DOI: https://doi.org/10.1107/S1744309113014036
• Primary Citation of Related Structures:  
  3W6G


• PubMed Abstract: 
  

  The crystal structure of peroxiredoxin from the anaerobic hyperthermophilic archaeon Pyrococcus horikoshii (PhPrx) was determined at a resolution of 2.25 Å. The overall structure was a ring-type decamer consisting of five homodimers. Citrate, which was included in the crystallization conditions, was bound to the peroxidatic cysteine of the active site, with two O atoms of the carboxyl group mimicking those of the substrate hydrogen peroxide. PhPrx lacked the C-terminal tail that forms a 32-residue extension of the protein in the homologous peroxiredoxin from Aeropyrum pernix (ApPrx).

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Organizational Affiliation: 

National Institute of Advanced Industrial Science and Technology, Ikeda, Osaka 563-8577, Japan. [e-mail]

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 PISA (software)

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 499.6 kDa 
• Atom Count: 35,926 
• Modelled Residue Count: 4,280 
• Deposited Residue Count: 4,320 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable peroxiredoxin	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T	216	Pyrococcus horikoshii OT3	Mutation(s): 0  Gene Names: PH1217 EC: 1.11.1.15 (PDB Primary Data), 1.11.1.24 (UniProt)
UniProt
Find proteins for O58966 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58966  Go to UniProtKB:  O58966

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC	AA [auth G], BA [auth H], CA [auth I], DA [auth J], EA [auth K], FA [auth L], GA [auth M], HA [auth N], IA [auth O], JA [auth P], KA [auth Q], LA [auth R], MA [auth S], NA [auth T], U [auth A], V [auth B], W [auth C], X [auth D], Y [auth E], Z [auth F]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.237 
• R-Value Work: 0.198 
• R-Value Observed: 0.198 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.354	α = 90
b = 94.733	β = 103.31
c = 228.204	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-10 
Deposition Author(s): Nakamura, T., Mori, A., Niiyama, M., Matsumura, H., Tokuyama, C., Morita, J., Uegaki, K., Inoue, T.

Revision History  

• Version 1.0: 2013-07-10
  Type: Initial release
  
• Version 1.1: 2013-12-11
  Changes: Database references
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations