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- PDB-7zxx: K563H Mutant of Recombinant CODH-II -

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Basic information

Entry
Database: PDB / ID: 7zxx
TitleK563H Mutant of Recombinant CODH-II
ComponentsCarbon monoxide dehydrogenase 2
KeywordsOXIDOREDUCTASE / CLUSTER C / 4FE-4S / CYTOPLASM / IRON / IRON-SULFUR / MEMBRANE / METAL-BINDING / NICKEL / DEHYDROGENASE
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 / Carbon monoxide dehydrogenase 2
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans Z-2901 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 23, 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

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Assembly

Deposited unit
X: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1116
Polymers67,0291
Non-polymers1,0815
Water9,044502
1
X: Carbon monoxide dehydrogenase 2
hetero molecules

X: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,22112
Polymers134,0592
Non-polymers2,16310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area9720 Å2
ΔGint-185 kcal/mol
Surface area38340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.840, 75.470, 71.340
Angle α, β, γ (deg.)90.000, 111.540, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-1171-

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: 67029.453 Da / Num. of mol.: 1 / Mutation: K563H
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, 507 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 2.09 Å3/Da / Density % sol: 41.12 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
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: Apr 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.4→40.78 Å / Num. obs: 105729 / % possible obs: 97.6 % / Redundancy: 3.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Net I/σ(I): 13.7
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 0.878 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 10361 / CC1/2: 0.576

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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: 1.4→37.735 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1478 1111 1.05 %
Rwork0.1158 104609 -
obs0.1162 105720 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 160.6 Å2 / Biso mean: 26.3314 Å2 / Biso min: 10.92 Å2
Refinement stepCycle: final / Resolution: 1.4→37.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4671 0 32 502 5205
Biso mean--30.3 38.88 -
Num. residues----635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124940
X-RAY DIFFRACTIONf_angle_d1.6116773
X-RAY DIFFRACTIONf_chiral_restr0.104808
X-RAY DIFFRACTIONf_plane_restr0.007877
X-RAY DIFFRACTIONf_dihedral_angle_d20.2591852
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4-1.46370.28091370.24291287296
1.4637-1.54090.22941370.17281288097
1.5409-1.63740.17851370.13661298697
1.6374-1.76390.1491390.10841304898
1.7639-1.94140.15071390.0971313698
1.9414-2.22220.14621400.09751317498
2.2222-2.79970.13961410.10481329099
2.7997-37.7350.13031410.11621322397

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