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- PDB-7zxj: K563A Mutant of Recombinant CODH-II -

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Basic information

Entry
Database: PDB / ID: 7zxj
TitleK563A 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 / 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: 1.249 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 21, 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)68,2198
Polymers66,9621
Non-polymers1,2567
Water16,592921
1
X: Carbon monoxide dehydrogenase 2
hetero molecules

X: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,43716
Polymers133,9252
Non-polymers2,51214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area11360 Å2
ΔGint-165 kcal/mol
Surface area38350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.096, 75.481, 71.265
Angle α, β, γ (deg.)90.000, 111.340, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-1170-

HOH

21X-1380-

HOH

31X-1535-

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: 66962.383 Da / Num. of mol.: 1 / Mutation: K563A
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: PLASMID / Details (production host): 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, 928 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
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 921 / 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: 41.34 %
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: 1.249→40.87 Å / Num. obs: 151514 / % possible obs: 99.1 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.09 / Net I/σ(I): 9.3
Reflection shellResolution: 1.25→1.29 Å / Rmerge(I) obs: 0.771 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 14296 / CC1/2: 0.662 / Rrim(I) all: 0.912

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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: 1.249→28.01 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1708 7568 5 %
Rwork0.1371 143799 -
obs0.1387 151367 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.77 Å2 / Biso mean: 18.0569 Å2 / Biso min: 3.52 Å2
Refinement stepCycle: final / Resolution: 1.249→28.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4666 0 69 923 5658
Biso mean--47.29 34.5 -
Num. residues----635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115198
X-RAY DIFFRACTIONf_angle_d1.4657159
X-RAY DIFFRACTIONf_chiral_restr0.092849
X-RAY DIFFRACTIONf_plane_restr0.007933
X-RAY DIFFRACTIONf_dihedral_angle_d20.52014
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.249-1.26280.36892080.335395483
1.2628-1.27760.30332550.25264839100
1.2776-1.29320.26532520.22624787100
1.2932-1.30960.24992530.21674804100
1.3096-1.32680.28192570.21314884100
1.3268-1.3450.23452540.19994827100
1.345-1.36420.23112500.19074751100
1.3642-1.38460.22972530.19184811100
1.3846-1.40620.25422560.18874860100
1.4062-1.42930.2312520.17874798100
1.4293-1.45390.21232550.17184849100
1.4539-1.48030.20352530.17054809100
1.4803-1.50880.19532540.15374808100
1.5088-1.53960.19212550.1444847100
1.5396-1.57310.16672540.14194832100
1.5731-1.60970.17262540.13834817100
1.6097-1.64990.1642530.13684822100
1.6499-1.69450.192520.13624790100
1.6945-1.74440.1862550.1344483399
1.7444-1.80070.15782510.1356477899
1.8007-1.8650.17972530.1434480599
1.865-1.93970.17432540.1298481299
1.9397-2.02790.15942520.12684802100
2.0279-2.13480.15112550.12744838100
2.1348-2.26850.16712520.123481599
2.2685-2.44360.13812530.1197479199
2.4436-2.68930.14162530.1169481499
2.6893-3.0780.14412550.117484199
3.078-3.87630.14032560.10294862100
3.8763-28.010.1452590.1221491999

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