2YYX

The Y65A mutant of tetraheme cytochrome c3 from Desulfovibrio Vulgaris Miyazaki F

PDB DOI: https://doi.org/10.2210/pdb2YYX/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Expression System: Shewanella oneidensis
Mutation(s): Yes

Deposited: 2007-05-02 Released: 2008-05-06
Deposition Author(s): Higuchi, Y., Komori, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free:
0.150 (DCC)
R-Value Work:
0.120 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structures of Noncoordinated Aromatic Residue Mutants in Tetraheme Cytochrome c3 from Desulfovibrio vulgaris Miyazaki F

Takayama, Y., Komori, H., Morita, K., Higuchi, Y., Akutsu, H.

To be published.

Macromolecule Content

Total Structure Weight: 13.93 kDa
Atom Count: 1,258
Modelled Residue Count: 107
Deposited Residue Count: 107
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 c3	A	107	Nitratidesulfovibrio vulgaris str. 'Miyazaki F	Mutation(s): 1
UniProt
Find proteins for P00132 (Nitratidesulfovibrio vulgaris (strain DSM 19637 / Miyazaki F)) Explore P00132 Go to UniProtKB: P00132
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00132
Sequence Annotations Expand
Reference Sequence LOADING

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] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free: 0.150 (DCC)
R-Value Work: 0.120 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.936	α = 90
b = 67.592	β = 90
c = 34.588	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
SHELX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-05-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-05-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-11-10
Changes: Database references, Derived calculations
Version 1.3: 2024-10-30
Changes: Data collection, Structure summary

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.