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- PDB-8on1: NI,FE-CODH -600mV state : 4 h Dioxygen Exposure -

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Basic information

Entry
Database: PDB / ID: 8on1
TitleNI,FE-CODH -600mV state : 4 h Dioxygen Exposure
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 / Carbon monoxide dehydrogenase 2
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans Z-2901 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsBasak, Y. / Jeoung, J.-H. / Dobbek, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)DO 785/6-2 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Stepwise O 2 -Induced Rearrangement and Disassembly of the [NiFe 4 (OH)( mu 3 -S) 4 ] Active Site Cluster of CO Dehydrogenase.
Authors: Basak, Y. / Jeoung, J.H. / Domnik, L. / Dobbek, H.
History
DepositionMar 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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)67,92710
Polymers67,0081
Non-polymers9189
Water10,665592
1
X: Carbon monoxide dehydrogenase 2
hetero molecules

X: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,85420
Polymers134,0172
Non-polymers1,83718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area10420 Å2
ΔGint-320 kcal/mol
Surface area37540 Å2
Unit cell
Length a, b, c (Å)112.410, 75.360, 71.350
Angle α, β, γ (deg.)90.00, 111.44, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-1338-

HOH

21X-1521-

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: 67008.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria)
Strain: Z-2901 / DSM 6008 / 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, 601 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-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe / 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 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 41.4 %
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: Nov 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.37→40.85 Å / Num. obs: 114390 / % possible obs: 97.9 % / Redundancy: 3.73 % / CC1/2: 0.999 / Net I/σ(I): 0.123
Reflection shellResolution: 1.37→1.42 Å / Num. unique obs: 10948 / CC1/2: 0.625

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→35.3 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1679 2000 1.75 %
Rwork0.126 --
obs0.1268 114332 97.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.37→35.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4655 0 19 592 5266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0164912
X-RAY DIFFRACTIONf_angle_d1.4586721
X-RAY DIFFRACTIONf_dihedral_angle_d16.4241844
X-RAY DIFFRACTIONf_chiral_restr1.43812
X-RAY DIFFRACTIONf_plane_restr0.013874
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.40.29851340.25947533X-RAY DIFFRACTION92
1.4-1.440.29581420.23867988X-RAY DIFFRACTION98
1.44-1.480.26311430.20438027X-RAY DIFFRACTION99
1.48-1.530.20241450.1688106X-RAY DIFFRACTION99
1.53-1.580.20211440.14658105X-RAY DIFFRACTION99
1.58-1.650.15141440.12928062X-RAY DIFFRACTION98
1.65-1.720.20631410.12437932X-RAY DIFFRACTION98
1.72-1.810.1711440.11598115X-RAY DIFFRACTION99
1.81-1.930.15881450.1198138X-RAY DIFFRACTION99
1.93-2.080.16181440.11438061X-RAY DIFFRACTION98
2.08-2.280.14421420.11048003X-RAY DIFFRACTION98
2.28-2.620.14161450.10838143X-RAY DIFFRACTION99
2.62-3.290.17351420.11948015X-RAY DIFFRACTION97
3.29-35.30.15131450.11938104X-RAY DIFFRACTION97

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