7XDN | pdb_00007xdn

Tunnel-redesigned O2-tolerant CO dehydrogenase for removal of CO in real flue gas (ChCODH2 A559H mutant in anaerobic condition)

• PDB DOI: https://doi.org/10.2210/pdb7XDN/pdb

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


• Deposited: 2022-03-28 Released: 2022-10-19 
• Deposition Author(s): Heo, Y.Y., Kim, S.M.
• Funding Organization(s): National Research Foundation (NRF, Korea)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.200 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

O2-tolerant CO dehydrogenase via tunnel redesign for the removal of CO from industrial flue gas

Kim, S.M., Lee, J.H., Kang, S.H., Heo, Y.Y., Yoon, H.J., Hahn, J.S., Lee, H.H., Kim, Y.H.

(2022) Nat Catal 5: 807-817

• DOI: https://doi.org/10.1038/s41929-022-00834-y

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: light scattering

Macromolecule Content 

• Total Structure Weight: 70.23 kDa 
• Atom Count: 5,181 
• 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	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NFS (Subject of Investigation/LOI)	D [auth A]	FE(4)-NI(1)-S(5) CLUSTER Fe4 Ni S5 DHBVHUGSWMHFLY-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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.200 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.859	α = 90
b = 76.026	β = 111.59
c = 71.613	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-10-19 
Deposition Author(s): Heo, Y.Y., Kim, S.M.

---

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	2015M3D3A1A01064919
National Research Foundation (NRF, Korea)	Korea, Republic Of	2020R1A5A1019631

Revision History  

• Version 1.0: 2022-10-19
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2026-08-12
  Type: Remediation
  Reason: Metalloprotein remediation
  Changes: Derived calculations, Structure summary