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- PDB-7zxl: H93A Mutant of Recombinant CODH-II -

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Basic information

Entry
Database: PDB / ID: 7zxl
TitleH93A 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: 1.2 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
Revision 2.0Oct 1, 2025Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_entry_details / struct_conn / struct_conn_type
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _pdbx_entry_details.has_protein_modification

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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)67,9876
Polymers66,9531
Non-polymers1,0345
Water15,061836
1
X: Carbon monoxide dehydrogenase 2
hetero molecules

X: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,97512
Polymers133,9072
Non-polymers2,06810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area9770 Å2
ΔGint-216 kcal/mol
Surface area38520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.330, 75.175, 71.354
Angle α, β, γ (deg.)90.000, 111.300, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-1365-

HOH

21X-1488-

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: 66953.422 Da / Num. of mol.: 1 / Mutation: H93A
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 , 6 types, 841 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 836 / 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: 2.1 Å3/Da / Density % sol: 41.32 %
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: 1.2→40.88 Å / Num. obs: 165542 / % possible obs: 96.1 % / Redundancy: 3.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.067 / Net I/σ(I): 12.8
Reflection shellResolution: 1.2→1.24 Å / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 13229 / CC1/2: 0.636 / Rrim(I) all: 0.812

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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: 1.2→26.164 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 13.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1378 8276 5 %
Rwork0.1127 157236 -
obs0.114 165512 96.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.64 Å2 / Biso mean: 21.9031 Å2 / Biso min: 8.39 Å2
Refinement stepCycle: final / Resolution: 1.2→26.164 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4665 0 27 840 5532
Biso mean--15.52 37.89 -
Num. residues----635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115479
X-RAY DIFFRACTIONf_angle_d1.4647579
X-RAY DIFFRACTIONf_chiral_restr0.101882
X-RAY DIFFRACTIONf_plane_restr0.0081006
X-RAY DIFFRACTIONf_dihedral_angle_d21.0882144
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.2001-1.21370.31321950.3115370668
1.2137-1.2280.28082250.2642426678
1.228-1.2430.26052410.243459485
1.243-1.25870.24262680.2179508093
1.2587-1.27520.22842780.2039528397
1.2752-1.29270.2142750.1892522397
1.2927-1.31120.22032770.18527297
1.3112-1.33080.20742780.1734528697
1.3308-1.35150.20142820.1617534798
1.3515-1.37370.18932760.1491523997
1.3737-1.39740.15932800.1426533398
1.3974-1.42280.17112810.1464532498
1.4228-1.45020.17012800.1385533498
1.4502-1.47980.15792800.1208532498
1.4798-1.51190.13352830.1018537198
1.5119-1.54710.1362820.0981536398
1.5471-1.58580.13532830.0959537299
1.5858-1.62870.11192820.0916536099
1.6287-1.67660.12962850.0906541199
1.6766-1.73070.12822830.0914536999
1.7307-1.79250.13342840.0925539799
1.7925-1.86430.12272830.0939538999
1.8643-1.94910.11732840.0874539699
1.9491-2.05180.11992860.0915542699
2.0518-2.18030.11592860.0911543399
2.1803-2.34860.10132860.0874542999
2.3486-2.58470.11642860.09225436100
2.5847-2.95830.11882880.10145480100
2.9583-3.72540.12642890.1015481100
3.7254-26.1640.12972900.118551299

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