PDB-9iyr: ChCODH2 A559W_V610H mutant in 1hour air exposure condition

ID or keywords:

Entry

Database: PDB / ID: 9iyr

Title

ChCODH2 A559W_V610H mutant in 1hour air exposure condition

Components

Carbon monoxide dehydrogenase 2

Keywords

OXIDOREDUCTASE / ELECTRON TRANSPORT

Function / homology

Function and homology information

anaerobic carbon monoxide dehydrogenase / hydroxylamine reductase activity / anaerobic carbon-monoxide dehydrogenase activity / nickel cation binding / generation of precursor metabolites and energy / peroxidase activity / response to hydrogen peroxide / 4 iron, 4 sulfur cluster binding / plasma membrane / cytoplasm
Similarity search - Function

Biological species

Carboxydothermus hydrogenoformans Z-2901 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.45 Å

Authors

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

Funding support

1items

Citation

Journal: To Be Published
Title: Air-viable, rapid CO dehydrogenase with a selectively sealed tunnel
Authors: Kong, S.Y. / Yoon, H.J. / Kim, S.M. / Lee, H.H.

History

Deposition	Jul 31, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 6, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9iyr.cif.gz	142.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9iyr.ent.gz	106.2 KB	Display	PDB format
PDBx/mmJSON format	9iyr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9iyr_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	9iyr_full_validation.pdf.gz	1.2 MB	Display
Data in XML	9iyr_validation.xml.gz	30.3 KB	Display
Data in CIF	9iyr_validation.cif.gz	43 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iy/9iyr ftp://data.pdbj.org/pub/pdb/validation_reports/iy/9iyr	HTTPS FTP

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Related structure data

Related structure data	9iylC 9iymC 9iynC 9iyoC 9iysC 9iytC 9iyuC 9iyvC 1su7S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#117 - Sep 2009 Xanthine Oxidoreductase similarity (1) #137 - May 2011 Cytochrome bc1 similarity (1) #144 - Dec 2011 Complex I similarity (1) #111 - Mar 2009 Hydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #36 - Dec 2002 Cytochrome c similarity (1) #82 - Oct 2006 Cytochrome p450 similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#117 - Sep 2009
Xanthine Oxidoreductase
similarity (1)
#137 - May 2011
Cytochrome bc1
similarity (1)
#144 - Dec 2011
Complex I
similarity (1)
#111 - Mar 2009
Hydrogenase
similarity (1)
#154 - Oct 2012
Citric Acid Cycle
similarity (1)
#36 - Dec 2002
Cytochrome c
similarity (1)
#82 - Oct 2006
Cytochrome p450
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: Carbon monoxide dehydrogenase 2

hetero molecules

70.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Carbon monoxide dehydrogenase 2

hetero molecules

A: Carbon monoxide dehydrogenase 2

hetero molecules

defined by author&software
Evidence: gel filtration, SEC-MALS
141 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	112.034, 76.168, 71.605
Angle α, β, γ (deg.)	90.00, 111.56, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-1081- HOH

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Protein , 1 types, 1 molecules A

#1: Protein	Carbon monoxide dehydrogenase 2 / CODH 2 Mass: 69346.039 Da / Num. of mol.: 1 / Mutation: A559W,V610H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria) Strain: Z-2901 / Gene: cooS2, cooSII, CHY_0085 / Production host: Escherichia coli (E. coli) References: UniProt: Q9F8A8, anaerobic carbon monoxide dehydrogenase

#1: Protein

Carbon monoxide dehydrogenase 2 / CODH 2

Mass: 69346.039 Da / Num. of mol.: 1 / Mutation: A559W,V610H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Carboxydothermus hydrogenoformans Z-2901 (bacteria)
Strain: Z-2901 / Gene: cooS2, cooSII, CHY_0085 / Production host:

Escherichia coli (E. coli)
References: UniProt: Q9F8A8, anaerobic carbon monoxide dehydrogenase

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Non-polymers , 5 types, 362 molecules

#2: Chemical	ChemComp-SF4 / IRON/SULFUR CLUSTER Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe₄S₄
#3: Chemical	ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe₂S₂
#4: Chemical	ChemComp-XCC / FE(4)-NI(1)-S(4) CLUSTER / C CLUSTER Mass: 410.333 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe₄NiS₄ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2 Å³/Da / Density % sol: 38.81 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: PEG3350, Magnesium chloride, Hepes/NaOH

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site: PAL/PLS

/ Beamline: 5C (4A) / Wavelength: 1 Å

Detector

Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 27, 2023

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.45→50 Å / Num. obs: 97777 / % possible obs: 98.7 % / Redundancy: 6.9 % / CC_1/2: 0.996 / CC star: 0.999 / R_merge(I) obs: 0.058 / R_pim(I) all: 0.024 / R_rim(I) all: 0.062 / Χ²: 1.036 / Net I/σ(I): 10.1 / Num. measured all: 670056

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.45-1.48	6.2	0.687	4827	0.85	0.959	0.292	0.748	0.439	97.2
1.48-1.5	6.8	0.57	4790	0.909	0.976	0.231	0.615	0.435	97.2
1.5-1.53	6.9	0.463	4776	0.933	0.982	0.186	0.5	0.457	97.6
1.53-1.56	7	0.426	4851	0.947	0.986	0.171	0.459	0.451	98
1.56-1.6	7.1	0.339	4806	0.957	0.989	0.136	0.366	0.479	98
1.6-1.63	7.1	0.281	4866	0.97	0.992	0.112	0.302	0.485	98.3
1.63-1.67	7	0.237	4843	0.976	0.994	0.096	0.256	0.52	98.4
1.67-1.72	7	0.199	4869	0.984	0.996	0.081	0.215	0.549	98.5
1.72-1.77	6.9	0.166	4867	0.988	0.997	0.067	0.179	0.594	98.7
1.77-1.83	6.7	0.136	4905	0.991	0.998	0.056	0.147	0.641	98.9
1.83-1.89	6.4	0.113	4875	0.993	0.998	0.048	0.123	0.721	99
1.89-1.97	6.1	0.099	4881	0.993	0.998	0.043	0.108	0.966	99
1.97-2.06	6.9	0.082	4954	0.996	0.999	0.033	0.089	0.896	99.3
2.06-2.17	7.3	0.073	4901	0.997	0.999	0.029	0.078	1.059	99.4
2.17-2.3	7.2	0.069	4922	0.997	0.999	0.028	0.075	1.579	99.6
2.3-2.48	7.2	0.055	4940	0.998	0.999	0.022	0.06	1.475	99.7
2.48-2.73	7.1	0.05	4949	0.998	0.999	0.02	0.054	1.662	99.8
2.73-3.12	6.8	0.045	4979	0.998	1	0.019	0.049	1.822	100
3.12-3.94	6.1	0.038	4978	0.998	1	0.017	0.042	2.05	99.9
3.94-50	7.4	0.04	4998	0.997	0.999	0.016	0.043	3.131	98.4

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
HKL-2000		data scaling
PDB_EXTRACT		data extraction
HKL-2000		data reduction
REFMAC		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1SU7

1su7

Resolution: 1.45→33.3 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.26 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2055	4963	5.09 %
R_work	0.1796	-	-
obs	0.1809	97589	98.4 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.45→33.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4687	0	0	358	5045

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	4778
X-RAY DIFFRACTION	f_angle_d	1.088	6504
X-RAY DIFFRACTION	f_dihedral_angle_d	6.133	671
X-RAY DIFFRACTION	f_chiral_restr	0.089	782
X-RAY DIFFRACTION	f_plane_restr	0.01	839

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.45-1.47	0.3027	141	0.275	2920	X-RAY DIFFRACTION	92
1.47-1.48	0.2512	157	0.2407	2972	X-RAY DIFFRACTION	97
1.48-1.5	0.2581	193	0.2248	3032	X-RAY DIFFRACTION	96
1.5-1.52	0.2486	140	0.213	3054	X-RAY DIFFRACTION	97
1.52-1.54	0.2387	153	0.2223	3062	X-RAY DIFFRACTION	97
1.54-1.56	0.2068	138	0.2177	3047	X-RAY DIFFRACTION	97
1.56-1.58	0.2329	163	0.2091	3081	X-RAY DIFFRACTION	98
1.58-1.61	0.2569	181	0.2086	3031	X-RAY DIFFRACTION	98
1.61-1.63	0.2389	167	0.2027	3039	X-RAY DIFFRACTION	98
1.63-1.66	0.2271	173	0.1964	3088	X-RAY DIFFRACTION	98
1.66-1.69	0.247	164	0.1906	3058	X-RAY DIFFRACTION	98
1.69-1.72	0.2022	170	0.1939	3053	X-RAY DIFFRACTION	98
1.72-1.75	0.2175	181	0.1915	3078	X-RAY DIFFRACTION	99
1.75-1.79	0.2242	168	0.1851	3106	X-RAY DIFFRACTION	99
1.79-1.83	0.2276	151	0.1905	3084	X-RAY DIFFRACTION	99
1.83-1.87	0.1874	171	0.1965	3097	X-RAY DIFFRACTION	99
1.87-1.92	0.229	159	0.192	3073	X-RAY DIFFRACTION	99
1.92-1.97	0.2245	172	0.1936	3094	X-RAY DIFFRACTION	99
1.97-2.02	0.2282	153	0.1916	3124	X-RAY DIFFRACTION	99
2.02-2.09	0.2274	160	0.1916	3132	X-RAY DIFFRACTION	99
2.09-2.16	0.1938	172	0.1844	3124	X-RAY DIFFRACTION	99
2.16-2.25	0.2016	155	0.1812	3129	X-RAY DIFFRACTION	100
2.25-2.35	0.2242	184	0.1836	3100	X-RAY DIFFRACTION	100
2.35-2.48	0.1754	160	0.1758	3153	X-RAY DIFFRACTION	100
2.48-2.63	0.2169	173	0.1792	3114	X-RAY DIFFRACTION	100
2.63-2.84	0.2077	189	0.1819	3160	X-RAY DIFFRACTION	100
2.84-3.12	0.2303	159	0.1892	3142	X-RAY DIFFRACTION	100
3.12-3.57	0.2152	172	0.1704	3172	X-RAY DIFFRACTION	100
3.57-4.5	0.1589	160	0.1446	3151	X-RAY DIFFRACTION	99
4.5-33.3	0.175	184	0.1558	3156	X-RAY DIFFRACTION	98

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