2WFC | pdb_00002wfc

Crystal structure of peroxiredoxin 5 from Arenicola Marina

PDB DOI: https://doi.org/10.2210/pdb2WFC/pdb

Classification: OXIDOREDUCTASE
Organism(s): Arenicola marina
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-04-03 Released: 2010-05-19
Deposition Author(s): Smeets, A., Declercq, J.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.213 (Depositor), 0.248 (DCC)
R-Value Work:
0.163 (Depositor), 0.207 (DCC)
R-Value Observed:
0.165 (Depositor)

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

Literature

Crystal Structure of Peroxiredoxin 5 from Arenicola Marina

Smeets, A., Knoops, B., Declercq, J.P.

To be published.

Macromolecule Content

Total Structure Weight: 70.12 kDa
Atom Count: 5,251
Modeled Residue Count: 636
Deposited Residue Count: 668
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEROXIREDOXIN 5	A, B, C, D	167	Arenicola marina	Mutation(s): 1 EC: 1.11.1.15 (PDB Primary Data), 1.11.1.24 (UniProt)
UniProt
Find proteins for Q1AN23 (Arenicola marina) Explore Q1AN23 Go to UniProtKB: Q1AN23
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q1AN23
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain E [auth C] MOL2 format, chain E [auth C] mmCIF format, chain E [auth C]	E [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth C] Interactions & Density Focus chain E [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.213 (Depositor), 0.248 (DCC)
R-Value Work: 0.163 (Depositor), 0.207 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.21	α = 90
b = 112.07	β = 97.35
c = 68.91	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-05-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-05-19
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

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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.