2CYM

EFFECTS OF AMINO ACID SUBSTITUTION ON THREE-DIMENSIONAL STRUCTURE: AN X-RAY ANALYSIS OF CYTOCHROME C3 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH AT 2 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Effects of amino acid substitution on three-dimensional structure: an X-ray analysis of cytochrome c3 from Desulfovibrio vulgaris Hildenborough at 2 A resolution.

Morimoto, Y.Tani, T.Okumura, H.Higuchi, Y.Yasuoka, N.

(1991) J.Biochem.(Tokyo) 110: 532-540


  • PubMed Abstract: 
  • The three-dimensional structure of cytochrome c3 from Desulfovibrio vulgaris Hildenborough has been determined by use of the molecular replacement method and refined at 2.0 A resolution. A suitable crystal of the cytochrome c3 was obtained from buffe ...

    The three-dimensional structure of cytochrome c3 from Desulfovibrio vulgaris Hildenborough has been determined by use of the molecular replacement method and refined at 2.0 A resolution. A suitable crystal of the cytochrome c3 was obtained from buffer solution (25 mM Tris-HCl, pH 7.4), with 75% ethanol as the precipitating reagent. Crystallographic data are as follows: a = 43.17 A, b = 62.91 A, c = 41.17 A, orthorhombic, P2(1)2(1)2(1) and Z = 4. Constrained least-squares refinement and a molecular dynamics procedure with a simulated structure annealing method yielded a crystallographic R-factor of 0.212. The similarity in the folding pattern of both cytochromes c3 is established, the mean deviation of the polypeptide backbone between the two structures being 0.367 A. Most of the amino acids substitutions from DvMF were located on the surface of the molecule, and in particular, S27 and V86 were placed near the propionic acid of the heme group so as to hang over the heme and the cleft of the molecule.


    Organizational Affiliation

    Department of Life Science, Faculty of Science, Himeji Institute of Technology, Hyogo.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C3
A
107Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303)Mutation(s): 0 
Find proteins for P00131 (Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303))
Go to UniProtKB:  P00131
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
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: 2 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.170α = 90.00
b = 62.910β = 90.00
c = 41.170γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
PROLSQrefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-04-30
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance