1JQK

Crystal structure of carbon monoxide dehydrogenase from Rhodospirillum rubrum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.259 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Life on carbon monoxide: X-ray structure of Rhodospirillum rubrum Ni-Fe-S carbon monoxide dehydrogenase.

Drennan, C.L.Heo, J.Sintchak, M.D.Schreiter, E.Ludden, P.W.

(2001) Proc Natl Acad Sci U S A 98: 11973-11978

  • DOI: 10.1073/pnas.211429998
  • Primary Citation of Related Structures:  
    1JQK

  • PubMed Abstract: 
  • A crystal structure of the anaerobic Ni-Fe-S carbon monoxide dehydrogenase (CODH) from Rhodospirillum rubrum has been determined to 2.8-A resolution. The CODH family, for which the R. rubrum enzyme is the prototype, catalyzes the biological oxidation of CO at an unusual Ni-Fe-S cluster called the C-cluster ...

    A crystal structure of the anaerobic Ni-Fe-S carbon monoxide dehydrogenase (CODH) from Rhodospirillum rubrum has been determined to 2.8-A resolution. The CODH family, for which the R. rubrum enzyme is the prototype, catalyzes the biological oxidation of CO at an unusual Ni-Fe-S cluster called the C-cluster. The Ni-Fe-S C-cluster contains a mononuclear site and a four-metal cubane. Surprisingly, anomalous dispersion data suggest that the mononuclear site contains Fe and not Ni, and the four-metal cubane has the form [NiFe(3)S(4)] and not [Fe(4)S(4)]. The mononuclear site and the four-metal cluster are bridged by means of Cys(531) and one of the sulfides of the cube. CODH is organized as a dimer with a previously unidentified [Fe(4)S(4)] cluster bridging the two subunits. Each monomer is comprised of three domains: a helical domain at the N terminus, an alpha/beta (Rossmann-like) domain in the middle, and an alpha/beta (Rossmann-like) domain at the C terminus. The helical domain contributes ligands to the bridging [Fe(4)S(4)] cluster and another [Fe(4)S(4)] cluster, the B-cluster, which is involved in electron transfer. The two Rossmann domains contribute ligands to the active site C-cluster. This x-ray structure provides insight into the mechanism of biological CO oxidation and has broader significance for the roles of Ni and Fe in biological systems.


    Organizational Affiliation

    Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. cdrennan@mit.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
carbon monoxide dehydrogenaseA, B, C, D, E, F639Rhodospirillum rubrumMutation(s): 0 
Gene Names: cooS
EC: 1.2.99.2 (PDB Primary Data), 1.2.7.4 (UniProt)
Find proteins for P31896 (Rhodospirillum rubrum)
Explore P31896 
Go to UniProtKB:  P31896
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
WCC
Query on WCC

Download Ideal Coordinates CCD File 
BA [auth E], FA [auth F], J [auth A], N [auth B], S [auth C], W [auth D]FE(3)-NI(1)-S(4) CLUSTER
Fe3 Ni S4
SEEZYPKDPRYISB-KUBGLCDSAO
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
AA [auth E] , EA [auth F] , H [auth A] , I [auth A] , M [auth B] , Q [auth C] , R [auth C] , V [auth D] , 
AA [auth E],  EA [auth F],  H [auth A],  I [auth A],  M [auth B],  Q [auth C],  R [auth C],  V [auth D],  Z [auth E]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FE2
Query on FE2

Download Ideal Coordinates CCD File 
DA [auth F], G [auth A], L [auth B], P [auth C], U [auth D], Y [auth E]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download Ideal Coordinates CCD File 
CA [auth E], GA [auth F], K [auth A], O [auth B], T [auth C], X [auth D]UNKNOWN ATOM OR ION
X
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.259 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.6α = 90
b = 200.1β = 111.5
c = 116.8γ = 90
Software Package:
Software NamePurpose
SOLVEphasing
SHARPphasing
DMmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-10-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance