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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
carbon monoxide dehydrogenase
A, B, C, D, E, F
A, B, C, D, E, F
639Rhodospirillum rubrumMutation(s): 0 
Gene Names: cooS
EC: 1.2.99.2 (PDB Primary Data), 1.2.7.4 (UniProt)
UniProt
Find proteins for P31896 (Rhodospirillum rubrum)
Explore P31896 
Go to UniProtKB:  P31896
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31896
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
WCC
Query on WCC
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BA [auth E],
FA [auth F],
J [auth A],
N [auth B],
S [auth C],
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
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AA [auth E],
EA [auth F],
H [auth A],
I [auth A],
M [auth B],
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
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DA [auth F],
G [auth A],
L [auth B],
P [auth C],
U [auth D],
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
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CA [auth E],
GA [auth F],
K [auth A],
O [auth B],
T [auth C],
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