1JAF

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

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

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

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

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

Entry History 

Deposition Data

• Released Date: 1998-01-21 
Deposition Author(s): Archer, M., Banci, L., Dikaya, E., Romao, M.J.

Revision History  

• 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