1JAF | pdb_00001jaf

CRYSTAL STRUCTURE OF CYTOCHROME C' FROM RHODOCYCLUS GELATINOSUS AT 2.5 ANGSTOMS RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb1JAF/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Rubrivivax gelatinosus
Mutation(s): No

Deposited: 1997-06-24 Released: 1998-01-21
Deposition Author(s): Archer, M., Banci, L., Dikaya, E., Romao, M.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.221 (Depositor)
R-Value Work:
0.179 (Depositor)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of Cytochrome C' from Rhodocyclus Gelatinosus and Comparison with Other Cytochromes C'

Archer, M., Banci, L., Dikaya, E., Romao, M.J.

(1997) J Biol Inorg Chem 2: 611

Macromolecule Content

Total Structure Weight: 27.84 kDa
Atom Count: 1,921
Modeled Residue Count: 256
Deposited Residue Count: 258
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME C'	A, B	129	Rubrivivax gelatinosus	Mutation(s): 0
UniProt
Find proteins for P00142 (Rubrivivax gelatinosus) Explore P00142 Go to UniProtKB: P00142
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00142
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 D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.221 (Depositor)
R-Value Work: 0.179 (Depositor)
R-Value Observed: 0.179 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.18	α = 90
b = 70.18	β = 90
c = 126.85	γ = 120

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 1998-01-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1998-01-21
Type: Initial release
Version 1.1: 2008-03-03
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-08-09
Changes: Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-09
Changes: Data collection, Structure summary

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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.