3B51 | pdb_00003b51

Ni,Fe-CODH-600 mV state

• PDB DOI: https://doi.org/10.2210/pdb3B51/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Carboxydothermus hydrogenoformans Z-2901
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-10-25 Released: 2007-12-11 
• Deposition Author(s): Jeoung, J.H., Dobbek, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.183 (Depositor) 
• R-Value Work: 
  0.157 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Literature

Carbon dioxide activation at the Ni,Fe-cluster of anaerobic carbon monoxide dehydrogenase.

Jeoung, J.H., Dobbek, H.

(2007) Science 318: 1461-1464

• PubMed: 18048691 
• DOI: https://doi.org/10.1126/science.1148481
• Primary Citation Related Structures: 
  3B51, 3B52, 3B53


• PubMed Abstract: 
  

  Anaerobic CO dehydrogenases catalyze the reversible oxidation of CO to CO2 at a complex Ni-, Fe-, and S-containing metal center called cluster C. We report crystal structures of CO dehydrogenase II from Carboxydothermus hydrogenoformans in three different states. In a reduced state, exogenous CO2 supplied in solution is bound and reductively activated by cluster C. In the intermediate structure, CO2 acts as a bridging ligand between Ni and the asymmetrically coordinated Fe, where it completes the square-planar coordination of the Ni ion. It replaces a water/hydroxo ligand bound to the Fe ion in the other two states. The structures define the mechanism of CO oxidation and CO2 reduction at the Ni-Fe site of cluster C.

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Organizational Affiliation: 
• Laboratorium Proteinkristallographie and Forschungszentrum für Bio-Makromoleküle, Universität Bayreuth, D-95440 Bayreuth, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 70.13 kDa 
• Atom Count: 5,656 
• Modeled Residue Count: 633 
• Deposited Residue Count: 656 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbon monoxide dehydrogenase 2	A [auth X]	656	Carboxydothermus hydrogenoformans Z-2901	Mutation(s): 0  Gene Names: cooS2, cooSII EC: 1.2.99.2 (PDB Primary Data), 1.2.7.4 (UniProt)
UniProt
Find proteins for Q9F8A8 (Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901)) Explore Q9F8A8  Go to UniProtKB:  Q9F8A8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WCC	D [auth X]	FE(3)-NI(1)-S(4) CLUSTER Fe3 Ni S4 SEEZYPKDPRYISB-UHFFFAOYSA-N
SF4	B [auth X]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
FES	C [auth X]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
FE2	E [auth X]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.183 (Depositor) 
• R-Value Work:  0.157 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.75	α = 90
b = 74.66	β = 111.28
c = 70.65	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-11 
Deposition Author(s): Jeoung, J.H., Dobbek, H.

Revision History  

• Version 1.0: 2007-12-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations