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- PDB-9fpn: Ni,Fe-CODH : Eu(II)-reduced pH 6.0 -

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Basic information

Entry
Database: PDB / ID: 9fpn
TitleNi,Fe-CODH : Eu(II)-reduced pH 6.0
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: 1.16 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)68,0646
Polymers67,0201
Non-polymers1,0445
Water13,836768
1
X: Carbon monoxide dehydrogenase 2
hetero molecules

X: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,12912
Polymers134,0412
Non-polymers2,08810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area10120 Å2
ΔGint-184 kcal/mol
Surface area37600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.328, 75.123, 71.080
Angle α, β, γ (deg.)90.00, 111.37, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-1721-

HOH

21X-1793-

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 , 6 types, 773 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-FE / FE (III) 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.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 768 / 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: 2.08 Å3/Da / Density % sol: 40.97 %
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: 14.2 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Feb 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.16→66.31 Å / Num. obs: 183196 / % possible obs: 96.4 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.117 / Rrim(I) all: 0.126 / Net I/σ(I): 9.2
Reflection shellResolution: 1.16→1.2 Å / Num. unique obs: 17754 / CC1/2: 0.348

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
MxCuBEdata collection
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.16→33.11 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1651 9168 5.02 %
Rwork0.1338 --
obs0.1353 182674 96.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.16→33.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4659 0 28 768 5455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135059
X-RAY DIFFRACTIONf_angle_d1.3476954
X-RAY DIFFRACTIONf_dihedral_angle_d12.9121930
X-RAY DIFFRACTIONf_chiral_restr1.431832
X-RAY DIFFRACTIONf_plane_restr0.013903
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.16-1.170.31563190.30845413X-RAY DIFFRACTION91
1.17-1.190.33652950.30395554X-RAY DIFFRACTION92
1.19-1.20.29412970.28265545X-RAY DIFFRACTION93
1.2-1.220.28093060.28385611X-RAY DIFFRACTION94
1.22-1.230.30853250.27455634X-RAY DIFFRACTION94
1.23-1.250.29773190.27215627X-RAY DIFFRACTION94
1.25-1.270.29232720.265665X-RAY DIFFRACTION95
1.27-1.290.30032990.25715670X-RAY DIFFRACTION95
1.29-1.310.24372980.23315676X-RAY DIFFRACTION95
1.31-1.330.27623330.22965714X-RAY DIFFRACTION95
1.33-1.350.22892930.22365742X-RAY DIFFRACTION95
1.35-1.370.24573040.20685679X-RAY DIFFRACTION96
1.37-1.40.24023050.19715783X-RAY DIFFRACTION96
1.4-1.430.21633190.18835723X-RAY DIFFRACTION96
1.43-1.460.20873210.17035772X-RAY DIFFRACTION96
1.46-1.490.18353000.15165775X-RAY DIFFRACTION96
1.49-1.530.16912920.1365822X-RAY DIFFRACTION97
1.53-1.570.15992670.12465896X-RAY DIFFRACTION97
1.57-1.620.1442910.11185800X-RAY DIFFRACTION97
1.62-1.670.15472920.1055871X-RAY DIFFRACTION97
1.67-1.730.14333210.10425832X-RAY DIFFRACTION97
1.73-1.80.1383260.09725827X-RAY DIFFRACTION98
1.8-1.880.13613000.09955943X-RAY DIFFRACTION98
1.88-1.980.13562760.10215921X-RAY DIFFRACTION98
1.98-2.110.14282890.10585973X-RAY DIFFRACTION98
2.11-2.270.12572850.10065949X-RAY DIFFRACTION98
2.27-2.50.13262980.09885995X-RAY DIFFRACTION99
2.5-2.860.12053360.10355969X-RAY DIFFRACTION99
2.86-3.60.13643210.11096035X-RAY DIFFRACTION99
3.6-33.110.15093690.11966090X-RAY DIFFRACTION100

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