2CCY

STRUCTURE OF FERRICYTOCHROME C(PRIME) FROM RHODOSPIRILLUM MOLISCHIANUM AT 1.67 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of ferricytochrome c' from Rhodospirillum molischianum at 1.67 A resolution.

Finzel, B.C.Weber, P.C.Hardman, K.D.Salemme, F.R.

(1985) J.Mol.Biol. 186: 627-643


  • PubMed Abstract: 
  • The structure of ferricytochrome c' from Rhodospirillum molischianum has been crystallographically refined to 1.67 A resolution using a combination of reciprocal space and restrained least-squares refinement methods. The final crystallographic R-fact ...

    The structure of ferricytochrome c' from Rhodospirillum molischianum has been crystallographically refined to 1.67 A resolution using a combination of reciprocal space and restrained least-squares refinement methods. The final crystallographic R-factor for 30,533 reflections measured with I greater than sigma (I) between infinity and 1.67 A is 0.188. The final model incorporates 1944 unique protein atoms (of a total of 1972) together with 194 bound solvent molecules. The structure has been analysed with respect to its detailed conformational properties, secondary structural features, temperature factor behavior, bound solvent sites, and heme geometry. The asymmetric unit of the cytochrome c' crystal contains a dimer composed of chemically identical 128-residue polypeptide chains. Although the refined structure shows the monomers to be very similar, examination of the differences that do occur allows an evaluation of how different lattice contacts affect protein conformation and solvent binding. In particular, comparison of solvent binding sites in the two subunits allows identification of a common set that are not altered by lattice interactions. The preservation of these solvent interactions in different lattice environments suggests that they play a structural role in protein stabilization in solution. The refined structure additionally reveals some new features that relate to the ligand binding properties and unusual mixed-spin state character of cytochrome c'. Finally, comparison of the heme binding geometry in cytochrome c' and other structurally unrelated c-type cytochromes shows that two alternative, but sterically favorable, conformational variants occur among the seven examples examined.


    Related Citations: 
    • Structural and Functional Diversity in 4-Alpha-Helical Proteins
      Weber, P.C.,Salemme, F.R.
      (1980) Nature 287: 82
    • Preliminary Crystallographic Data for Cytochromes C(Prime) of Rhodopseudomonas Capsulata and Rhodospirillum Molischianum
      Weber, P.,Salemme, F.R.
      (1977) J.Mol.Biol. 117: 815
    • Correlations between Structural and Spectroscopic Properties of the High-Spin Heme Protein Cytochrome C(Prime)
      Weber, P.C.
      (1982) Biochemistry 21: 5116
    • Structure of Cytochrome C(Prime). A Dimeric, High-Spin Haem Protein
      Weber, P.C.,Bartsch, R.G.,Cusanovich, M.A.,Hamlin, R.C.,Howard, A.,Jordan, S.R.,Kamen, M.D.,Meyer, T.E.,Weatherford, D.W.,Xuong, N.H.,Salemme, F.R.
      (1980) Nature 286: 302
    • Lattice Mobility and Anomalous Temperature Factor Behaviour in Cytochrome C(Prime)
      Finzel, B.C.,Salemme, F.R.
      (1985) Nature 315: 686
    • Crystallographic Structure of Rhodospirillum Molischianum Ferricytochrome C(Prime) at 2.5 Angstroms Resolution
      Weber, P.C.,Howard, A.,Xuong, N.H.,Salemme, F.R.
      (1981) J.Mol.Biol. 153: 399
    • On the Evolutionary Relationship of the 4-Alpha-Helical Heme Proteins. The Comparison of Cytochrome B562 and Cytochrome C(Prime)
      Weber, P.C.,Salemme, F.R.,Mathews, F.S.,Bethge, P.H.
      (1981) J.Biol.Chem. 256: 7702



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C
A, B
128Phaeospirillum molischianumMutation(s): 0 
Find proteins for P00152 (Phaeospirillum molischianum)
Go to UniProtKB:  P00152
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 56.580α = 90.00
b = 72.330β = 90.00
c = 75.440γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1986-01-21
    Type: Initial release
  • Version 1.1: 2008-03-10
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other