1CGN

CYTOCHROME C'


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Three-dimensional structure of cytochrome c' from two Alcaligenes species and the implications for four-helix bundle structures.

Dobbs, A.J.Anderson, B.F.Faber, H.R.Baker, E.N.

(1996) Acta Crystallogr.,Sect.D 52: 356-368

  • DOI: 10.1107/S0907444995008328
  • Primary Citation of Related Structures:  1CGO
  • Also Cited By: 1E83, 1E84, 1E85, 1E86

  • PubMed Abstract: 
  • The three-dimensional structures of two cytochromes c' have been determined in order to analyse the common features of proteins of this family and their relationship with other four-helix bundle structures. The structure of cytochrome c' from Alcalig ...

    The three-dimensional structures of two cytochromes c' have been determined in order to analyse the common features of proteins of this family and their relationship with other four-helix bundle structures. The structure of cytochrome c' from Alcaligenes sp was determined by molecular replacement supplemented with the iron anomalous scattering and the use of a single isomorphous heavy-atom derivative, and was refined using synchrotron data to 1.8 A resolution. The final model, comprising 956 protein atoms (one monomer) and 89 water molecules, has a final R value of 0.188 for all data in the range 20.0-1.8 A resolution (14 673 reflections). The structure of the cytochrome c' from Alcaligenes denitrificans is isomorphous and essentially identical (r.m.s. deviation for all atoms 0.36 A). Although its amino-acid sequence has not been determined chemically, only four differences from that of Alcaligenes sp cytochrome c' were identified by the X-ray analysis. The final model for Alcaligenes denitrificans cytochrome c', comprising 953 protein atoms and 75 water molecules, gave a final R factor of 0.167 for all data in the range 20.0-2.15 A (8220 reflections). The cytochrome c' monomer forms a classic four-helix bundle, determined by the packing of hydrophobic side chains around the enclosed haem group. There are very few cross-linking hydrogen bonds between the helices, the principal side-chain hydrogen bonding involving one of the haem propionates and a conserved Arg residue. The cytochrome c' dimer is created by a crystallographic twofold axis. Monomer-monomer contacts primarily involve the two A helices, with size complementarity of side chains in a central solvent-excluded portion of the interface and hydrogen bonding at the periphery. Both species have a pyroglutamic acid N-terminal residue. The haem iron is five-coordinate, 0.32 A out of the haem plane towards the fifth ligand, His120. The unusual magnetic properties of the Fe atom may be linked to a conserved basic residue, Arg124, adjacent to His120.


    Related Citations: 
    • The Amino Acid Sequence of Cytochrome C' from Alcaligenes Sp. N.C.I.B. 11015
      Ambler, R.P.
      (1973) Biochem.J. 135: 751
    • Atomic Structure of a Cytochrome C' with an Unusual Ligand-Controlled Dimer Dissociation at 1.8 Angstroms Resolution
      Ren, Z.,Meyer, T.E.,Mcree, D.E.
      (1993) J.Mol.Biol. 234: 433
    • Structure of Ferricytochrome C' from Rhodospirillum Molischianum at 1.67 Angstroms
      Finzel, B.C.,Weber, P.C.,Hardman, K.D.,Salemme, F.R.
      (1985) J.Mol.Biol. 186: 627
    • Crystallographic Structure of Rhodospirillum Molischianum Ferricytochrome C' at 2.5 Angstroms Resolution
      Weber, P.C.,Howard, A.,Xoung, N.H.,Salemme, F.R.
      (1981) J.Mol.Biol. 353: 399
    • Three-Dimensional Structure of Ferricytochrome C' from Rhodospirillum Rubrum at 2.8 Angstroms Resolution
      Yasui, M.,Harada, S.,Kai, Y.,Kasai, N.,Kusunoki, M.,Matsura, Y.
      (1992) J.Biochem.(Tokyo) 111: 317


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Massey University, Palmerston North, New Zealand.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C
A
127Alcaligenes xylosoxydans xylosoxydansN/A
Find proteins for P00138 (Alcaligenes xylosoxydans xylosoxydans)
Go to UniProtKB:  P00138
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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 54.600α = 90.00
b = 54.600β = 90.00
c = 180.400γ = 120.00
Software Package:
Software NamePurpose
SUPPLIEDdata reduction
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-07-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance