9IYM | pdb_00009iym

ChCODH2 A559W_V610H mutant

• PDB DOI: https://doi.org/10.2210/pdb9IYM/pdb

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


• Deposited: 2024-07-31 Released: 2025-08-06 
• Deposition Author(s): Kong, S.Y., Yoon, H.J., Kim, S.M., Lee, H.H.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.208 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Air-viable, rapid CO dehydrogenase with a selectively sealed tunnel

Kong, S.Y., Yoon, H.J., Kim, S.M., Lee, H.H.

To be published.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 70.34 kDa 
• Atom Count: 5,006 
• 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	656	Carboxydothermus hydrogenoformans Z-2901	Mutation(s): 2  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
XCC	D [auth A]	FE(4)-NI(1)-S(4) CLUSTER Fe4 Ni S4 QGLWBXDZIHZONR-UHFFFAOYSA-N
SF4	B [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
FES	C [auth A]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
FE	E [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free:  0.208 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.738	α = 90
b = 75.745	β = 111.3
c = 71.428	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-06 
Deposition Author(s): Kong, S.Y., Yoon, H.J., Kim, S.M., Lee, H.H.

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Funding Organization	Location	Grant Number
Other government		--

Revision History  

• Version 1.0: 2025-08-06
  Type: Initial release