8X9E

Crystal structure of CO dehydrogenase mutant with increased affinity for electron mediators in low PEG concentration

• PDB DOI: https://doi.org/10.2210/pdb8X9E/pdb

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


• Deposited: 2023-11-30 Released: 2024-04-17 
• Deposition Author(s): Lee, H.H., Heo, Y., Yoon, H.J., Kim, S.M., Kong, S.Y.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.227 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 

Literature

Identifying a key spot for electron mediator-interaction to tailor CO dehydrogenase's affinity

Kim, S.M., Kang, S.H., Lee, J., Heo, Y., Poloniataki, E.G., Kang, J., Yoon, H.J., Kong, S.Y., Yun, Y., Kim, H., Ryu, J., Lee, H.H., Kim, Y.H.

(2024) Nat Commun 15: 2732

• DOI: https://doi.org/10.1038/s41467-024-46909-1

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: 70.12 kDa 
• Atom Count: 4,806 
• Modelled 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 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 5 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
EDO	F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FE	E [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.227 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.083	α = 90
b = 75.088	β = 111.39
c = 71.14	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-17 
Deposition Author(s): Lee, H.H., Heo, Y., Yoon, H.J., Kim, S.M., Kong, S.Y.

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Funding Organization	Location	Grant Number
Other government	Korea, Republic Of	--

Revision History  

• Version 1.0: 2024-04-17
  Type: Initial release