7ZY1

I567A Mutant of Recombinant CODH-II

• PDB DOI: https://doi.org/10.2210/pdb7ZY1/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Carboxydothermus hydrogenoformans Z-2901
• Expression System: Escherichia coli B
• Mutation(s): Yes 


• Deposited: 2022-05-23 Released: 2023-03-15 
• Deposition Author(s): Basak, Y., Jeoung, J.H., Dobbek, H.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free: 0.144 
• R-Value Work: 0.129 
• R-Value Observed: 0.129 

Starting Model: experimental

Literature

Substrate Activation at the Ni,Fe Cluster of CO Dehydrogenases: The Influence of the Protein Matrix

Basak, Y., Jeoung, J.H., Domnik, L., Ruickoldt, J., Dobbek, H.

(2022) ACS Catal 

• DOI: https://doi.org/10.1021/acscatal.2c02922

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: 67.92 kDa 
• Atom Count: 5,779 
• Modelled Residue Count: 633 
• Deposited Residue Count: 636 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbon monoxide dehydrogenase 2	A [auth X]	636	Carboxydothermus hydrogenoformans Z-2901	Mutation(s): 1  Gene Names: cooS2, cooSII, CHY_0085 EC: 1.2.7.4
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 (Subject of Investigation/LOI)	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: 1.43 Å
• R-Value Free: 0.144 
• R-Value Work: 0.129 
• R-Value Observed: 0.129 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.669	α = 90
b = 75.809	β = 111.11
c = 71.5	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing
MxCuBE	data collection

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-03-15 
Deposition Author(s): Basak, Y., Jeoung, J.H., Dobbek, H.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	DFG DO 785/6-2

Revision History  

• Version 1.0: 2023-03-15
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection, Refinement description