2PWJ | pdb_00002pwj

Structure of a mitochondrial type II peroxiredoxin from Pisum sativum

PDB DOI: https://doi.org/10.2210/pdb2PWJ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Lathyrus oleraceus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-05-11 Released: 2008-05-27
Deposition Author(s): Lopez-Jaramillo, F.J., Barranco-Medina, S., Lazaro, J.J., Santoyo-Gonzalez, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.292 (Depositor), 0.287 (DCC)
R-Value Work:
0.277 (Depositor), 0.274 (DCC)
R-Value Observed:
0.298 (Depositor)

Starting Model: in silico
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This is version 1.3 of the entry. See complete history.

Literature

Structure of a mitochondrial type II peroxiredoxin from Pisum sativum

Lopez-Jaramillo, F.J., Barranco-Medina, S., Lazaro, J.J., Santoyo-Gonzalez, F.

To be published.

Macromolecule Content

Total Structure Weight: 110.79 kDa
Atom Count: 7,476
Modeled Residue Count: 975
Deposited Residue Count: 1,026
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial peroxiredoxin	A, B, C, D, E A, B, C, D, E, F	171	Lathyrus oleraceus	Mutation(s): 0 Gene Names: prx EC: 1.11.1.15 (PDB Primary Data), 1.11.1.25 (UniProt)
UniProt
Find proteins for Q6KBB1 (Pisum sativum) Explore Q6KBB1 Go to UniProtKB: Q6KBB1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6KBB1
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.292 (Depositor), 0.287 (DCC)
R-Value Work: 0.277 (Depositor), 0.274 (DCC)
R-Value Observed: 0.298 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.88	α = 102.94
b = 66.4	β = 104.44
c = 77.23	γ = 99.07

Software Package:

Software Name	Purpose
SAINT	data scaling
AMoRE	phasing
CNS	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data collection
SAINT	data reduction
XPREP	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-05-27

Deposition Author(s):

Lopez-Jaramillo, F.J.

Barranco-Medina, S.

Santoyo-Gonzalez, F.

Revision History (Full details and data files)

Version 1.0: 2008-05-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references
Version 1.3: 2026-03-04
Changes: Data collection, Refinement description, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.