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- PDB-9fpf: Ni,Fe-CODH : Ti(III)-reduced pH 8.0 -

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Basic information

Entry
Database: PDB / ID: 9fpf
TitleNi,Fe-CODH : Ti(III)-reduced pH 8.0
ComponentsCarbon monoxide dehydrogenase 2
KeywordsOXIDOREDUCTASE / C-CLUSTER / 4FE-4S / IRON / IRON-SULFUR / METAL-BINDING / NICKEL / NICKEL REDOX / CARBON DIOXIDE / CARBON MONOXIDE / CODH
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
Ni-containing CO dehydrogenase / CO dehydrogenase, alpha-bundle / Hydroxylamine reductase/Ni-containing CO dehydrogenase / Prismane/CO dehydrogenase family / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily
Similarity search - Domain/homology
: / FE2/S2 (INORGANIC) CLUSTER / DI(HYDROXYETHYL)ETHER / IRON/SULFUR CLUSTER / FE(3)-NI(1)-S(4) CLUSTER / Carbon monoxide dehydrogenase 2
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans Z-2901 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsBasak, Y. / Jeoung, J.-H. / Dobbek, H.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)DO 785/6-2 Germany
Germanys Excellence StrategyEXC 2008 - 390540038 - UniSysCat Germany
CitationJournal: Nature Catalysis / Year: 2025
Title: Ni,Fe-CODH : Ti(III)-reduced pH 8.0
Authors: Basak, Y. / Jeoung, J.-H. / Dobbek, H.
History
DepositionJun 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2938
Polymers67,0201
Non-polymers1,2727
Water9,692538
1
X: Carbon monoxide dehydrogenase 2
hetero molecules

X: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,58516
Polymers134,0412
Non-polymers2,54414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area10610 Å2
ΔGint-189 kcal/mol
Surface area38830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.780, 75.240, 71.450
Angle α, β, γ (deg.)90.00, 111.50, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-1364-

HOH

21X-1521-

HOH

31X-1570-

HOH

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Components

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Protein , 1 types, 1 molecules X

#1: Protein Carbon monoxide dehydrogenase 2 / CODH 2


Mass: 67020.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria)
Strain: Z-2901 / DSM 6008 / Gene: cooS2, cooSII, CHY_0085 / Plasmid: PET28A / Production host: Escherichia coli B (bacteria) / Strain (production host): ROSSETTA DE3
References: UniProt: Q9F8A8, anaerobic carbon monoxide dehydrogenase

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Non-polymers , 7 types, 545 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 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.55 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES pH 7.5, PEG 2000MME 14-18%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.27→40.87 Å / Num. obs: 144583 / % possible obs: 99.4 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Rrim(I) all: 0.108 / Net I/σ(I): 10.9
Reflection shellResolution: 1.27→1.32 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 14260 / CC1/2: 0.389 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
XSCALEdata scaling
XDSdata reduction
Cootmodel building
MxCuBEdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.27→33.24 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.165 7221 5 %
Rwork0.1462 --
obs0.1471 144520 98.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.27→33.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4665 0 43 538 5246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085204
X-RAY DIFFRACTIONf_angle_d1.0517155
X-RAY DIFFRACTIONf_dihedral_angle_d14.2421988
X-RAY DIFFRACTIONf_chiral_restr0.083847
X-RAY DIFFRACTIONf_plane_restr0.01933
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.280.36331830.37043504X-RAY DIFFRACTION75
1.28-1.30.35322370.3594520X-RAY DIFFRACTION99
1.3-1.310.3692390.35034558X-RAY DIFFRACTION98
1.31-1.330.33042420.3124581X-RAY DIFFRACTION99
1.33-1.350.29392390.3014565X-RAY DIFFRACTION99
1.35-1.370.29152400.27824573X-RAY DIFFRACTION99
1.37-1.390.28352430.26754613X-RAY DIFFRACTION99
1.39-1.410.24762400.25724572X-RAY DIFFRACTION99
1.41-1.430.27312430.24194606X-RAY DIFFRACTION99
1.43-1.450.24582410.23674575X-RAY DIFFRACTION99
1.45-1.480.27382440.23394638X-RAY DIFFRACTION99
1.48-1.50.21982410.22284595X-RAY DIFFRACTION99
1.5-1.530.21232410.19544566X-RAY DIFFRACTION100
1.53-1.560.2162420.17034604X-RAY DIFFRACTION100
1.56-1.60.1712440.15644640X-RAY DIFFRACTION100
1.6-1.640.19552440.15314623X-RAY DIFFRACTION100
1.64-1.680.17132440.1394638X-RAY DIFFRACTION100
1.68-1.720.15362430.1364618X-RAY DIFFRACTION100
1.72-1.770.16282440.13064636X-RAY DIFFRACTION100
1.77-1.830.15162460.12824669X-RAY DIFFRACTION100
1.83-1.890.16172410.1254585X-RAY DIFFRACTION100
1.89-1.970.14812430.12584625X-RAY DIFFRACTION100
1.97-2.060.13722430.12514615X-RAY DIFFRACTION99
2.06-2.170.14242440.12114633X-RAY DIFFRACTION100
2.17-2.30.13462430.1174620X-RAY DIFFRACTION100
2.3-2.480.12972460.1154660X-RAY DIFFRACTION100
2.48-2.730.14842440.12014647X-RAY DIFFRACTION99
2.73-3.130.16222440.1324633X-RAY DIFFRACTION99
3.13-3.940.13432440.12814638X-RAY DIFFRACTION99
3.94-33.240.14442490.13074749X-RAY DIFFRACTION100

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