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- PDB-7zxc: H96D Mutant of Recombinant CODH-II -

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Basic information

Entry
Database: PDB / ID: 7zxc
TitleH96D Mutant of Recombinant CODH-II
ComponentsCarbon monoxide dehydrogenase 2
KeywordsOXIDOREDUCTASE / CLUSTER C / 4FE-4S / CYTOPLASM / IRON / IRON-SULFUR / MEMBRANE / METAL-BINDING / NICKEL
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 / 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: 1.696 Å
AuthorsBasak, Y. / Jeoung, J.H. / Dobbek, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)DFG DO 785/6-2 Germany
CitationJournal: Acs Catalysis / Year: 2022
Title: Substrate Activation at the Ni,Fe Cluster of CO Dehydrogenases: The Influence of the Protein Matrix
Authors: Basak, Y. / Jeoung, J.H. / Domnik, L. / Ruickoldt, J. / Dobbek, H.
History
DepositionMay 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)67,9355
Polymers66,9971
Non-polymers9384
Water12,971720
1
X: Carbon monoxide dehydrogenase 2
hetero molecules

X: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,87010
Polymers133,9952
Non-polymers1,8768
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area9390 Å2
ΔGint-199 kcal/mol
Surface area38050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.700, 75.240, 71.220
Angle α, β, γ (deg.)90.000, 111.380, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-1255-

HOH

21X-1360-

HOH

31X-1369-

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: 66997.430 Da / Num. of mol.: 1 / Mutation: H96D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria)
Strain: ATCC BAA-161 / DSM 6008 / Z-2901 / 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 , 5 types, 724 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 720 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 41.38 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris pH 6.5, PEG 3350 10-18%, Ammonium sulphate 0.18M

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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 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.696→19.874 Å / Num. obs: 61373 / % possible obs: 98.5 % / Redundancy: 4.02 % / CC1/2: 0.998 / Rmerge(I) obs: 0.116 / Rrim(I) all: 0.108 / Net I/σ(I): 11.07
Reflection shellResolution: 1.696→1.72 Å / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 0.54 / Num. unique obs: 2047 / CC1/2: 0.381 / Rrim(I) all: 0.378

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
MxCuBEdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B51

3b51


Resolution: 1.696→19.874 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 19.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2049 2984 5 %
Rwork0.1629 56688 -
obs0.165 59672 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.08 Å2 / Biso mean: 17.5634 Å2 / Biso min: 1.46 Å2
Refinement stepCycle: final / Resolution: 1.696→19.874 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4668 0 22 720 5410
Biso mean--10.16 28.38 -
Num. residues----635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015038
X-RAY DIFFRACTIONf_angle_d1.4396905
X-RAY DIFFRACTIONf_chiral_restr0.067820
X-RAY DIFFRACTIONf_plane_restr0.006896
X-RAY DIFFRACTIONf_dihedral_angle_d22.1491906
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.696-1.72380.3927980.3707186268
1.7238-1.75350.31751450.2785268497
1.7535-1.78530.27031370.247270797
1.7853-1.81960.26911430.2185268798
1.8196-1.85680.24091430.2118266798
1.8568-1.89710.2591390.2059269998
1.8971-1.94120.27631390.2274275598
1.9412-1.98970.22731440.177270199
1.9897-2.04340.20871470.1725272599
2.0434-2.10350.23411490.1885272298
2.1035-2.17130.21871380.1608273699
2.1713-2.24880.21651460.1721273399
2.2488-2.33870.2131420.155274899
2.3387-2.4450.20931450.13772741100
2.445-2.57360.17631450.13292766100
2.5736-2.73450.18581510.13682797100
2.7345-2.9450.18461440.14622769100
2.945-3.24020.18021450.13912777100
3.2402-3.70650.16611480.12752772100
3.7065-4.65980.15311450.11312806100
4.6598-19.8740.15911510.1398283499

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