155C | pdb_0000155c

THE STRUCTURE OF PARACOCCUS DENITRIFICANS CYTOCHROME C550


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 
    0.429 (DCC) 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

The structure of Paracoccus denitrificans cytochrome c550.

Timkovich, R.Dickerson, R.E.

(1976) J Biological Chem 251: 4033-4046

  • DOI: https://doi.org/10.2210/pdb155c/pdb
  • Primary Citation Related Structures: 
    155C

  • PubMed Abstract: 

    The crystal structure of Paracoccus (formerly Micrococcus) denitrificans cytochrome c550 has been solved by x-ray diffraction to a resolution of 2.45 A. In both amino acid sequence and molecular structure it is evolutionarily homologous with mitochondrial cytochrome c from eukaryotes and photosynthetic cytochrome c2 from purple non-sulfur bacteria. All of these cytochromes c have the same basic folding pattern, with surface insertions of extra amino acids in c550. Various strains of c2 have all, some, or none of the extra insertions observed in c550. The hydrophobic heme environment, position of aromatic rings, and structure and environment of the heme crevice, are virtually identical in cytochromes c55o, c, and c2. Radical changes observed at all regions on the molecular surface except the heme crevice argue for the importance of the crevice and the exposed edge of the heme in the transfer of electrons to and from the cytochrome molecule.

Macromolecule Content 

  • Total Structure Weight: 14.89 kDa 
  • Atom Count: 1,017 
  • Modeled Residue Count: 135 
  • Deposited Residue Count: 135 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CYTOCHROME C550135Paracoccus denitrificansMutation(s): 0 
UniProt
Find proteins for P00096 (Paracoccus denitrificans)
Explore P00096 
Go to UniProtKB:  P00096
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00096
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM

Query on HEM



Download:Ideal Coordinates CCD File
B [auth A]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 Work:  0.429 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.7α = 90
b = 82.17β = 90
c = 31.56γ = 90

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1976-08-20
    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: 2024-06-05
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 1.4: 2024-10-16
    Changes: Structure summary