5C9M | pdb_00005c9m

The structure of oxidized rat cytochrome c (T28A) at 1.362 angstroms resolution.

PDB DOI: https://doi.org/10.2210/pdb5C9M/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Rattus norvegicus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2015-06-28 Released: 2016-09-21
Deposition Author(s): Edwards, B.F.P., Mahapatra, G., Vaishnav, A.A., Brunzelle, J.S., Huttemann, M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.36 Å
R-Value Free:
0.170 (Depositor), 0.168 (DCC)
R-Value Work:
0.129 (Depositor), 0.129 (DCC)
R-Value Observed:
0.131 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

The structure of oxidized rat cytochrome c (T28A) at 1.362 angstroms resolution.

Edwards, B.F.P., Mahapatra, G., Vaishnav, A.A., Brunzelle, J.S., Huttemann, M.

To be published.

Macromolecule Content

Total Structure Weight: 49.72 kDa
Atom Count: 3,944
Modeled Residue Count: 416
Deposited Residue Count: 420
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c, somatic	A, B, C, D	105	Rattus norvegicus	Mutation(s): 1 Gene Names: Cycs
UniProt
Find proteins for P62898 (Rattus norvegicus) Explore P62898 Go to UniProtKB: P62898
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62898
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] SDF format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D] mmCIF format, chain E [auth A]	E [auth A], G [auth B], J [auth C], L [auth D]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D]
FC6 Query on FC6 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain K [auth C] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C]	F [auth A], H [auth B], I [auth B], K [auth C]	HEXACYANOFERRATE(3-) C₆ Fe N₆ HCMVSLMENOCDCK-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.36 Å
R-Value Free: 0.170 (Depositor), 0.168 (DCC)
R-Value Work: 0.129 (Depositor), 0.129 (DCC)
R-Value Observed: 0.131 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.517	α = 109.86
b = 52.567	β = 92.93
c = 61.771	γ = 92.2

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	phasing
Aimless	data scaling
XDS	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-09-21

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	NIGMS RO1 089900

Revision History (Full details and data files)

Version 1.0: 2016-09-21
Type: Initial release
Version 1.1: 2017-09-06
Changes: Author supporting evidence, Derived calculations
Version 1.2: 2017-11-01
Changes: Author supporting evidence
Version 1.3: 2019-12-25
Changes: Author supporting evidence, Derived calculations
Version 1.4: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2024-10-23
Changes: Structure summary