PDBsum entry 1cgo

Electron transport (cytochrome)

PDB id: 1cgo

Contents

Protein chain

125 a.a. *

Ligands

HEC

Waters ×89

* Residue conservation analysis

PDB id:

1cgo

Name:

Electron transport (cytochrome)

Title:

Cytochrome c'

Structure:

CytochromE C. Chain: a. Engineered: yes

Source:

Alcaligenes sp.. Organism_taxid: 512

Biol. unit:

Dimer (from PQS)

Resolution:

1.80Å R-factor: 0.188

Authors:

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

Key ref:

A.J.Dobbs et al. (1996). Three-dimensional structure of cytochrome c' from two Alcaligenes species and the implications for four-helix bundle structures. Acta Crystallogr D Biol Crystallogr, 52, 356-368. PubMed id: 15299707 DOI: 10.1107/S0907444995008328

Date:

01-May-95 Release date: 31-Jul-95

Protein chain

P00138  (CYCP_ALCXX) -  Cytochrome c' from Alcaligenes xylosoxydans xylosoxydans

Seq: 127 a.a.

Struc: 125 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DOI no: 10.1107/S0907444995008328

Acta Crystallogr D Biol Crystallogr 52:356-368 (1996)

PubMed id: 15299707

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

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

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 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.

Selected figure(s)

Figure 1.
Fig. 1. Variation of the crystallographic R factor with resolution for the cytochromes c' from Alcaligenes sp (full line) and Alcaligenes denitrificans (broken line). he teoretical variation for coordinate errors of (a) 0.10, (b) 0.15 and (c) 0.20,~ (Luzzati, 1952) is shown.

Figure 6.
Fig. 6. Stereoview showing the environment of the conserved Argl2 side chain and te inner of the two haem propionate groups. Hdrogen bonds are shown with broken ines.

Figure 14.
IMET . L P A A F P E G

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1996, 52, 356-368) copyright 1996.

Figures were selected by an automated process.