3CYR

CYTOCHROME C3 FROM DESULFOVIBRIO DESULFURICANS ATCC 27774P

PDB DOI: https://doi.org/10.2210/pdb3CYR/pdb
Entry: 3CYR supersedes: 2CYR

Classification: ELECTRON TRANSPORT
Organism(s): Desulfovibrio desulfuricans
Mutation(s): No

Deposited: 1997-07-24 Released: 1998-01-28
Deposition Author(s): Simoes, P., Matias, P.M., Morais, J., Wilson, K., Dauter, Z., Carrondo, M.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.221
R-Value Observed: 0.175

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Refinement of the Three-Dimensional Structures of Cytochrome C3 from Desulfovibrio Vulgaris Hildenborough at 1.67 Angstroms Resolution and from Desulfovibrio Desulfuricans Atcc 27774 at 1.6 Angstroms Resolution

Simoes, P., Matias, P.M., Morais, J., Wilson, K., Dauter, Z., Carrondo, M.A.

(1998) Inorganica Chim Acta 273: 213-224

Macromolecule Content

Total Structure Weight: 14.06 kDa
Atom Count: 1,061
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	Desulfovibrio desulfuricans	Mutation(s): 0
UniProt
Find proteins for Q9L915 (Desulfovibrio desulfuricans) Explore Q9L915 Go to UniProtKB: Q9L915
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9L915
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] 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]	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: 1.60 Å
R-Value Free: 0.221
R-Value Observed: 0.175
Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.71	α = 90
b = 62.71	β = 90
c = 111.09	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
MOSFLM	data reduction
CCP4	data scaling
ROTAVATA	data scaling
X-PLOR	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 1998-01-28

Deposition Author(s):

This entry supersedes: 2CYR

Revision History (Full details and data files)

Version 1.0: 1998-01-28
Type: Initial release
Version 1.1: 2008-03-25
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-08-09
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

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Deposit Data

Help and Resources

3CYR

CYTOCHROME C3 FROM DESULFOVIBRIO DESULFURICANS ATCC 27774P

Refinement of the Three-Dimensional Structures of Cytochrome C3 from Desulfovibrio Vulgaris Hildenborough at 1.67 Angstroms Resolution and from Desulfovibrio Desulfuricans Atcc 27774 at 1.6 Angstroms Resolution

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)