3R99 | pdb_00003r99

Joint Neutron and X-ray structure of Cytochrome c peroxidase

PDB DOI: https://doi.org/10.2210/pdb3R99/pdb

Classification: OXIDOREDUCTASE
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-03-25 Released: 2012-04-04
Deposition Author(s): Blakeley, M.P., Fisher, S.J., Gumiero, A., Moody, P.C.E., Raven, E.L.

Experimental Data Snapshot

Method: NEUTRON DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.250 (Depositor)
R-Value Work:
0.207 (Depositor)
R-Value Observed:
0.211 (Depositor)

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.203 (Depositor), 0.230 (DCC)
R-Value Work:
0.166 (Depositor), 0.160 (DCC)
R-Value Observed:
0.170 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Hydrogen bonds in heme peroxidases: a combined X-ray and neutron study of cytochrome c peroxidase

Gumiero, A., Blakeley, M.P., Metcalfe, C.L., Murphy, E.J., Raven, E.L., Moody, P.C.E.

To be published.

Macromolecule Content

Total Structure Weight: 34.09 kDa
Atom Count: 2,584
Modeled Residue Count: 293
Deposited Residue Count: 293
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c peroxidase	A	293	Saccharomyces cerevisiae	Mutation(s): 0 EC: 1.11.1.5
UniProt
Find proteins for P00431 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00431 Go to UniProtKB: P00431
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00431
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: NEUTRON DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.250 (Depositor)
R-Value Work: 0.207 (Depositor)
R-Value Observed: 0.211 (Depositor)

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.203 (Depositor), 0.230 (DCC)
R-Value Work: 0.166 (Depositor), 0.160 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.547	α = 90
b = 76.655	β = 90
c = 107.078	γ = 90

Software Package:

Software Name	Purpose
QLD	data collection
PHENIX	model building
PHENIX	refinement
LAUEGEN	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-04-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-04-04
Type: Initial release
Version 1.1: 2018-03-07
Changes: Data collection
Version 1.2: 2018-05-16
Changes: Data collection
Version 1.3: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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.