PDB-9tox: CO dehydrogenase 2 variant A559W

ID or keywords:

Entry

Database: PDB / ID: 9tox

Title

CO dehydrogenase 2 variant A559W

Components

Carbon monoxide dehydrogenase 2

Keywords

OXIDOREDUCTASE / CODH / channel / A559W / CLUSTER C / 4FE-4S / IRON / IRON-SULFUR / NICKEL

Function / homology

Function and homology information

anaerobic carbon monoxide dehydrogenase / hydroxylamine reductase activity / anaerobic carbon-monoxide dehydrogenase activity / nickel cation binding / peroxidase activity / response to hydrogen peroxide / generation of precursor metabolites and energy / 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: 1.49 Å

Authors

Gebhardt, P. / Dobbek, H. / Jeoung, J.-H.

Funding support

Germany, 1items

Citation

Journal: Angew.Chem.Int.Ed.Engl. / Year: 2026
Title: Correspondence on "Fortification of FeS Clusters Reshapes Anaerobic CO Dehydrogenase Into an Air-Viable Enzyme Through Multilayered Sealing of O 2 Tunnels".
Authors: Opdam, L.V. / Gebhardt, P. / Leger, C. / Dobbek, H. / Fourmond, V.

History

Deposition	Dec 17, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 3, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9tox.cif.gz	303.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9tox.ent.gz	203.6 KB	Display	PDB format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/to/9tox ftp://data.pdbj.org/pub/pdb/validation_reports/to/9tox	HTTPS FTP

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Related structure data

Related structure data	9tp0C 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 /

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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

X: Carbon monoxide dehydrogenase 2

hetero molecules

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

1

X: Carbon monoxide dehydrogenase 2

hetero molecules

X: Carbon monoxide dehydrogenase 2

hetero molecules

defined by author&software
135 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	111.31, 75.33, 71.59
Angle α, β, γ (deg.)	90, 111.56, 90
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	X-972- HOH

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Protein , 1 types, 1 molecules X

#1: Protein	Carbon monoxide dehydrogenase 2 / CODH 2 Mass: 66776.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria) Gene: cooS2, cooSII, CHY_0085 / Production host: Escherichia coli B (bacteria) References: UniProt: Q9F8A8, anaerobic carbon monoxide dehydrogenase

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Non-polymers , 5 types, 186 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-WCC / FE(3)-NI(1)-S(4) CLUSTER / C CLUSTER CUBANE Mass: 354.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe₃NiS₄
#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.: 182 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
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: 2.09 Å³/Da / Density % sol: 41.15 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: PEG 2000MME

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 13, 2025
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.91841 Å / Relative weight: 1
Reflection	Resolution: 1.49→40.77 Å / Num. obs: 175782 / % possible obs: 99.4 % / Redundancy: 3.41 % / CC_1/2: 0.998 / Net I/σ(I): 9.81
Reflection shell	Resolution: 1.49→1.58 Å / Num. unique obs: 28446 / CC_1/2: 0.322

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0431 (refmacat 0.4.123)	refinement
PHASER		phasing
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.49→40.799 Å / Cor.coef. F_o:F_c: 0.973 / Cor.coef. F_o:F_c free: 0.954 / SU B: 5.141 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.075
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2126	1071	1.196 %	RANDOM
R_work	0.1749	88496	-	-
all	0.175	-	-	-
obs	-	89567	99.88 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.3 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 13.54 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.576 Å²	-0 Å²	-0.486 Å²
2-	-	-1.246 Å²	0 Å²
3-	-	-	0.803 Å²

Refinement step

Cycle: LAST / Resolution: 1.49→40.799 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4663	0	21	182	4866

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.017	4877
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	4785
X-RAY DIFFRACTION	r_angle_refined_deg	2.048	1.84	6650
X-RAY DIFFRACTION	r_angle_other_deg	0.482	1.56	11027
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	9.322	5.18	694
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.953	10	832
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.631	10	180
X-RAY DIFFRACTION	r_chiral_restr	0.37	0.2	801
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	5714
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	986
X-RAY DIFFRACTION	r_nbd_refined	0.223	0.2	1051
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.19	0.2	4488
X-RAY DIFFRACTION	r_nbtor_refined	0.165	0.2	2433
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.074	0.2	2614
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.125	0.2	194
X-RAY DIFFRACTION	r_metal_ion_refined	0.151	0.2	11
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.158	0.2	40
X-RAY DIFFRACTION	r_nbd_other	0.173	0.2	179
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.082	0.2	35
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.157	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	4.306	1.047	2575
X-RAY DIFFRACTION	r_mcbond_other	4.303	1.047	2575
X-RAY DIFFRACTION	r_mcangle_it	4.95	1.872	3228
X-RAY DIFFRACTION	r_mcangle_other	4.951	1.872	3229
X-RAY DIFFRACTION	r_scbond_it	8.97	1.488	2302
X-RAY DIFFRACTION	r_scbond_other	9.012	1.487	2274
X-RAY DIFFRACTION	r_scangle_it	10.083	2.479	3392
X-RAY DIFFRACTION	r_scangle_other	10.101	2.471	3374
X-RAY DIFFRACTION	r_lrange_it	9.194	11.203	5413
X-RAY DIFFRACTION	r_lrange_other	9.212	10.827	5378

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.49-1.529	0.353	79	0.375	6508	0.375	6596	0.886	0.877	99.8636	0.377
1.529-1.571	0.353	77	0.348	6336	0.348	6413	0.897	0.901	100	0.347
1.571-1.616	0.295	74	0.316	6162	0.315	6240	0.937	0.921	99.9359	0.31
1.616-1.666	0.329	73	0.275	6022	0.275	6097	0.928	0.943	99.9672	0.264
1.666-1.72	0.217	70	0.254	5823	0.253	5893	0.963	0.954	100	0.238
1.72-1.78	0.257	68	0.224	5634	0.225	5702	0.955	0.966	100	0.199
1.78-1.848	0.278	66	0.199	5423	0.2	5491	0.958	0.974	99.9636	0.168
1.848-1.923	0.22	64	0.177	5257	0.178	5326	0.971	0.98	99.9061	0.143
1.923-2.008	0.198	60	0.171	4976	0.172	5045	0.978	0.981	99.8216	0.139
2.008-2.106	0.186	58	0.16	4847	0.16	4909	0.977	0.984	99.9185	0.13
2.106-2.219	0.148	55	0.148	4550	0.148	4611	0.987	0.987	99.8699	0.121
2.219-2.354	0.18	53	0.138	4333	0.139	4388	0.983	0.988	99.9544	0.115
2.354-2.516	0.166	49	0.129	4053	0.129	4103	0.981	0.99	99.9756	0.109
2.516-2.716	0.216	46	0.138	3800	0.139	3852	0.973	0.989	99.8442	0.117
2.716-2.974	0.193	42	0.152	3494	0.153	3539	0.977	0.986	99.9152	0.134
2.974-3.323	0.203	38	0.159	3154	0.159	3200	0.976	0.985	99.75	0.146
3.323-3.833	0.211	34	0.16	2815	0.16	2855	0.974	0.984	99.7898	0.153
3.833-4.684	0.201	29	0.136	2386	0.137	2417	0.978	0.989	99.9173	0.142
4.684-6.581	0.222	23	0.168	1856	0.168	1886	0.977	0.985	99.6288	0.176
6.581-40.799	0.171	13	0.162	1067	0.162	1089	0.987	0.982	99.1736	0.187

Refinement TLS params.

Method: refined / Origin x: 56.71 Å / Origin y: 14.766 Å / Origin z: 48.16 Å

	11	12	13	21	22	23	31	32	33
T	0.0905 Å²	-0.0293 Å²	-0.0417 Å²	-	0.2029 Å²	0.0153 Å²	-	-	0.0224 Å²
L	0.852 °²	0.3413 °²	0.3173 °²	-	0.7917 °²	-0.0004 °²	-	-	0.5792 °²
S	0.0339 Å °	-0.1361 Å °	-0.0398 Å °	0.1947 Å °	-0.0691 Å °	-0.1196 Å °	-0.1438 Å °	0.0638 Å °	0.0352 Å °

Refinement TLS group

Selection: ALL

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