1CRY | pdb_00001cry

APPLICATION OF AN AUTOMATIC MOLECULAR REPLACEMENT PROCEDURE TO CRYSTAL STRUCTURE OF CYTOCHROME C2 FROM RHODOPSEUDOMONAS VIRIDIS

• PDB DOI: https://doi.org/10.2210/pdb1CRY/pdb

• Classification: ELECTRON TRANSPORT(HEME PROTEIN)
• Organism(s): Blastochloris viridis
• Mutation(s): No 


• Deposited: 1993-12-27 Released: 1994-04-30 
• Deposition Author(s): Miki, K., Sogabe, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Work: 
  0.219 (Depositor) 
• R-Value Observed: 
  0.219 (Depositor) 

Literature

Application of an automatic molecular-replacement procedure to crystal structure analysis of cytochrome c2 from Rhodopseudomonas viridis.

Miki, K., Sogabe, S., Uno, A., Ezoe, T., Kasai, N., Saeda, M., Matsuura, Y., Miki, M.

(1994) Acta Crystallogr D Biol Crystallogr 50: 271-275

• PubMed: 15299438 
• DOI: https://doi.org/10.1107/S0907444993013952
• Primary Citation Related Structures: 
  1CRY


• PubMed Abstract: 
  

  An automatic molecular-replacement procedure has been applied to solve the crystal structure of cytochrome c(2) from Rhodopseudomonas viridis. The structure was solved on the basis of the structure of tuna cytochrome c as a search model using an automatic processing program system, AUTOMR. The refinements by molecular dynamics and restrained least-squares methods result in a current crystallographic R factor of 0.219 for diffraction data at 3 A resolution.

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Organizational Affiliation: 
• Research Laboratory of Resources Utilization, Tokyo Institute of Technology, Yokohama, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 12.29 kDa 
• Atom Count: 864 
• Modeled Residue Count: 107 
• Deposited Residue Count: 107 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME C2	A	107	Blastochloris viridis	Mutation(s): 0
UniProt
Find proteins for P00083 (Blastochloris viridis) Explore P00083  Go to UniProtKB:  P00083

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC	B [auth A]	HEME C C34 H36 Fe N4 O4 YZTICFPLOXKSQO-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Work:  0.219 (Depositor) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.13	α = 90
b = 76.13	β = 90
c = 40.4	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
PROLSQ	refinement
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-04-30 
Deposition Author(s): Miki, K., Sogabe, S.

Revision History  

• Version 1.0: 1994-04-30
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.4: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.5: 2019-08-14
  Changes: Data collection, Refinement description
• Version 2.0: 2021-03-03
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-10-09
  Changes: Data collection, Database references, Structure summary
• Version 3.0: 2026-08-12
  Type: Remediation
  Reason: Metalloprotein remediation
  Changes: Advisory, Data collection, Derived calculations, Non-polymer description, Structure summary