1COT

X-RAY STRUCTURE OF THE CYTOCHROME C2 ISOLATED FROM PARACOCCUS DENITRIFICANS REFINED TO 1.7 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

X-Ray structure of the cytochrome c2 isolated from Paracoccus denitrificans refined to 1.7-A resolution.

Benning, M.M.Meyer, T.E.Holden, H.M.

(1994) Arch Biochem Biophys 310: 460-466

  • DOI: https://doi.org/10.1006/abbi.1994.1193
  • Primary Citation of Related Structures:  
    1COT

  • PubMed Abstract: 

    The cytochrome c2 (formerly c550) isolated from Paracoccus denitrificans is one of the larger bacterial c-type proteins examined thus far. The molecular structure of this cytochrome has been redetermined and refined to 1.7-A resolution with a crystallographic R-factor of 17.5% for all measured X-ray data. Like other, smaller c-type cytochromes, the molecule consists of five alpha-helices that wrap around the heme group. In addition, this bacterial cytochrome contains two strands of anti-parallel beta-sheet, five Type I turns, and three Type II turns. The present model differs from the originally determined structure in several regions including the N-terminus, the loop delineated by Asp 25 to Lys 31, the region defined by Trp 86 to Val 88, and the C-terminus. A total of 103 water molecules has been positioned into the electron density map. Six of these waters are directly involved in heme binding.


  • Organizational Affiliation

    Institute for Enzyme Research, Graduate School, University of Wisconsin, Madison 53705.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C2129Paracoccus 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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
B [auth A]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.6α = 90
b = 42.1β = 90
c = 81.6γ = 90
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-09-30
    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 2.0: 2021-03-03
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary