9IYS | pdb_00009iys

ChCODH2 A559W_V610H mutant in 2hour air exposure condition

PDB DOI: https://doi.org/10.2210/pdb9IYS/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.202 (Depositor), 0.201 (DCC)
R-Value Work:
0.175 (Depositor), 0.173 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
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This is version 1.0 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 70.34 kDa
Atom Count: 5,062
Modeled Residue Count: 633
Deposited Residue Count: 656
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9F8A8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XCC Query on XCC Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	FE(4)-NI(1)-S(4) CLUSTER Fe₄ Ni S₄ QGLWBXDZIHZONR-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.202 (Depositor), 0.201 (DCC)
R-Value Work: 0.175 (Depositor), 0.173 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.344	α = 90
b = 76.511	β = 111.1
c = 71.103	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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-08-06

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government		--

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.