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- PDB-7zy1: I567A Mutant of Recombinant CODH-II -

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Basic information

Entry
Database: PDB / ID: 7zy1
TitleI567A 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 / 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: 1.434 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)67,9165
Polymers66,9781
Non-polymers9384
Water14,700816
1
X: Carbon monoxide dehydrogenase 2
hetero molecules

X: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,83210
Polymers133,9572
Non-polymers1,8768
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area9500 Å2
ΔGint-200 kcal/mol
Surface area38010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.669, 75.809, 71.500
Angle α, β, γ (deg.)90.000, 111.110, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-1324-

HOH

21X-1425-

HOH

31X-1428-

HOH

41X-1615-

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: 66978.406 Da / Num. of mol.: 1 / Mutation: I567A
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 , 5 types, 820 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 816 / 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: 2.11 Å3/Da / Density % sol: 41.64 %
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: Mar 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.43→41.01 Å / Num. obs: 100997 / % possible obs: 99.4 % / Redundancy: 3.69 % / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.068 / Net I/σ(I): 11.7
Reflection shellResolution: 1.43→1.49 Å / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 9818 / CC1/2: 0.707 / Rrim(I) all: 0.633

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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: 1.434→34.24 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 14.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1441 1098 1.09 %
Rwork0.1292 99890 -
obs0.1294 100988 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.84 Å2 / Biso mean: 23.0375 Å2 / Biso min: 5.9 Å2
Refinement stepCycle: final / Resolution: 1.434→34.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4651 0 23 816 5490
Biso mean--12.49 42.21 -
Num. residues----633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095095
X-RAY DIFFRACTIONf_angle_d1.4766998
X-RAY DIFFRACTIONf_chiral_restr0.081827
X-RAY DIFFRACTIONf_plane_restr0.007920
X-RAY DIFFRACTIONf_dihedral_angle_d19.051931
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4342-1.49950.25891340.24881219598
1.4995-1.57860.19871380.192912543100
1.5786-1.67750.19161370.156412458100
1.6775-1.8070.16211370.142412515100
1.807-1.98880.16431380.124212531100
1.9888-2.27650.14021380.117712499100
2.2765-2.8680.1121370.10931251699
2.868-34.240.12861390.11811263399
Refinement TLS params.Method: refined / Origin x: 99.7683 Å / Origin y: 12.4188 Å / Origin z: 81.1639 Å
111213212223313233
T0.0607 Å2-0.0125 Å20.0005 Å2-0.0553 Å20.0023 Å2--0.0495 Å2
L0.3002 °20.1108 °20.0781 °2-0.3169 °2-0.0784 °2--0.18 °2
S0.0046 Å °-0.0366 Å °-0.0224 Å °0.0661 Å °-0.0146 Å °-0.0392 Å °-0.0733 Å °0.0436 Å °-0.004 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allX4 - 636
2X-RAY DIFFRACTION1allX637 - 1457

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