3W6G | pdb_00003w6g

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.237 (Depositor), 0.237 (DCC)
R-Value Work:
0.198 (Depositor), 0.198 (DCC)
R-Value Observed:
0.198 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1744309113014036
Primary Citation 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).

Organizational Affiliation

National Institute of Advanced Industrial Science and Technology, Ikeda, Osaka 563-8577, Japan. nakamura-t@aist.go.jp

Macromolecule Content

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

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable peroxiredoxin	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O58966
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain BA [auth H] SDF format, chain DA [auth J] SDF format, chain GA [auth M] SDF format, chain KA [auth Q] SDF format, chain LA [auth R] SDF format, chain MA [auth S] SDF format, chain U [auth A] SDF format, chain V [auth B] SDF format, chain W [auth C] SDF format, chain X [auth D] SDF format, chain Y [auth E] SDF format, chain Z [auth F] SDF format, chain NA [auth T] SDF format, chain JA [auth P] SDF format, chain IA [auth O] SDF format, chain HA [auth N] SDF format, chain FA [auth L] SDF format, chain EA [auth K] SDF format, chain CA [auth I] SDF format, chain AA [auth G] MOL2 format, chain BA [auth H] MOL2 format, chain DA [auth J] MOL2 format, chain GA [auth M] MOL2 format, chain KA [auth Q] MOL2 format, chain LA [auth R] MOL2 format, chain MA [auth S] MOL2 format, chain U [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth F] MOL2 format, chain NA [auth T] MOL2 format, chain JA [auth P] MOL2 format, chain IA [auth O] MOL2 format, chain HA [auth N] MOL2 format, chain FA [auth L] MOL2 format, chain EA [auth K] MOL2 format, chain CA [auth I] MOL2 format, chain AA [auth G] mmCIF format, chain BA [auth H] mmCIF format, chain DA [auth J] mmCIF format, chain GA [auth M] mmCIF format, chain KA [auth Q] mmCIF format, chain LA [auth R] mmCIF format, chain MA [auth S] mmCIF format, chain U [auth A] mmCIF format, chain V [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth F] mmCIF format, chain NA [auth T] mmCIF format, chain JA [auth P] mmCIF format, chain IA [auth O] mmCIF format, chain HA [auth N] mmCIF format, chain FA [auth L] mmCIF format, chain EA [auth K] mmCIF format, chain CA [auth I] mmCIF format, chain AA [auth G]	AA [auth G] BA [auth H] CA [auth I] DA [auth J] EA [auth K] 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		Interactions Focus chain AA [auth G] Focus chain BA [auth H] Focus chain CA [auth I] Focus chain DA [auth J] Focus chain EA [auth K] Focus chain FA [auth L] Focus chain GA [auth M] Focus chain HA [auth N] Focus chain IA [auth O] Focus chain JA [auth P] Focus chain KA [auth Q] Focus chain LA [auth R] Focus chain MA [auth S] Focus chain NA [auth T] Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth C] Focus chain X [auth D] Focus chain Y [auth E] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth H] Focus chain CA [auth I] Focus chain DA [auth J] Focus chain EA [auth K] Focus chain FA [auth L] Focus chain GA [auth M] Focus chain HA [auth N] Focus chain IA [auth O] Focus chain JA [auth P] Focus chain KA [auth Q] Focus chain LA [auth R] Focus chain MA [auth S] Focus chain NA [auth T] Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth C] Focus chain X [auth D] Focus chain Y [auth E] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.237 (Depositor), 0.237 (DCC)
R-Value Work: 0.198 (Depositor), 0.198 (DCC)
R-Value Observed: 0.198 (Depositor)

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

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-07-10

Deposition Author(s):

Revision History (Full details and data files)

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