3OZZ | pdb_00003ozz

Structure of a cytochrome b5 core-swap mutant

PDB DOI: https://doi.org/10.2210/pdb3OZZ/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Bos taurus
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2010-09-27 Released: 2011-09-14
Deposition Author(s): Terzyan, S., Parthasarathy, S., Zhang, X.C., Benson, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.229 (Depositor), 0.224 (DCC)
R-Value Work:
0.176 (Depositor), 0.172 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Structure of a cytochrome b5 core-swap mutant

Parthasarathy, S., Terzyan, S., Zhang, X.C., Benson, D.

To be published.

Macromolecule Content

Total Structure Weight: 10.06 kDa
Atom Count: 907
Modeled Residue Count: 82
Deposited Residue Count: 82
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b5	A [auth B]	82	Bos taurus	Mutation(s): 12 Gene Names: CYB5, CYB5A, Cyb5b, Cyb5m, Omb5
UniProt
Find proteins for P00171 (Bos taurus) Explore P00171 Go to UniProtKB: P00171
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00171
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 MOL2 format, chain B mmCIF format, chain B	B	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.229 (Depositor), 0.224 (DCC)
R-Value Work: 0.176 (Depositor), 0.172 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.669	α = 90
b = 30.654	β = 95.65
c = 23.553	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-09-14

Deposition Author(s):

Parthasarathy, S.

Revision History (Full details and data files)

Version 1.0: 2011-09-14
Type: Initial release
Version 1.1: 2023-09-06
Changes: Data collection, Database references, Derived calculations, 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.