2J9B

THE CRYSTAL STRUCTURE OF CYTOCHROME C' FROM RUBRIVIVAX GELATINOSUS AT 1.5 A RESOLUTION AND PH 6.3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.153 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

High resolution crystal structure of Rubrivivax gelatinosus cytochrome c'.

Benini, S.Rypniewski, W.R.Wilson, K.S.Ciurli, S.

(2008) J. Inorg. Biochem. 102: 1322-1328

  • DOI: 10.1016/j.jinorgbio.2008.01.017
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structure of the cytochrome c' from the purple non-sulfur phototrophic bacterium Rubrivivax gelatinosus was determined using two crystals grown independently at pH 6.3 and pH 8. The resolution attained for the two structures (1.29 A and 1.50 A fo ...

    The structure of the cytochrome c' from the purple non-sulfur phototrophic bacterium Rubrivivax gelatinosus was determined using two crystals grown independently at pH 6.3 and pH 8. The resolution attained for the two structures (1.29 A and 1.50 A for the crystals at high and low pH, respectively) is the highest to date for this class of proteins. The two structures were compared in detail in an attempt to investigate the influence of pH on the geometry of the haem and of the coordination environment of the Fe(III) ion. However, while the results suggest some small propensity for the movement of the metal atom out of the plane of the haem ring upon pH increase, the accuracy of the measurements at these two pH below the pK of the axial histidine is not sufficient to provide hard evidence of a shift in the iron position and associated changes.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Diffraction Analysis of Cytochrome C' from Rubrivivax Gelatinosus at 1.3 A Resolution.
      Benini, S.,Rypniewski, W.R.,Wilson, K.S.,Ciurli, S.
      (1998) Acta Crystallogr.,Sect.D 54: 284


    Organizational Affiliation

    York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5YW, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C'
A, B
129Rubrivivax gelatinosusMutation(s): 0 
Find proteins for P00142 (Rubrivivax gelatinosus)
Go to UniProtKB:  P00142
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download SDF File 
Download CCD File 
A, B
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.153 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 69.558α = 90.00
b = 69.558β = 90.00
c = 123.374γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
AMoREphasing
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-12-04
    Type: Initial release
  • Version 1.1: 2012-06-06
    Type: Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
  • Version 1.2: 2012-06-13
    Type: Other
  • Version 2.0: 2019-01-23
    Type: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary