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- PDB-7b9a: CooS-V with Xe-soaked -

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Basic information

Entry
Database: PDB / ID: 7b9a
TitleCooS-V with Xe-soaked
ComponentsCarbon monoxide dehydrogenase
KeywordsOXIDOREDUCTASE / Hybrid cluster / HCP / CODH
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 / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #30 / Rossmann fold - #2030 / 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 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #30 / Rossmann fold - #2030 / 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 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / FE2/S2 (INORGANIC) CLUSTER / HYDROSULFURIC ACID / IRON/SULFUR CLUSTER / Chem-T2N / XENON / Carbon monoxide dehydrogenase
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsJeoung, J.H. / Dobbek, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)390540038 Germany
Citation
Journal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: A Morphing [4Fe-3S-nO]-Cluster within a Carbon Monoxide Dehydrogenase Scaffold.
Authors: Jeoung, J.H. / Fesseler, J. / Domnik, L. / Klemke, F. / Sinnreich, M. / Teutloff, C. / Dobbek, H.
#1: Journal: To Be Published
Title: Hybrid cluster protein CooS-V
Authors: Jeoung, J.H. / Dobbek, H.
History
DepositionDec 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 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

Downloads & links

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Assembly

Deposited unit
A: Carbon monoxide dehydrogenase
B: Carbon monoxide dehydrogenase
C: Carbon monoxide dehydrogenase
D: Carbon monoxide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)286,136101
Polymers273,1514
Non-polymers12,98597
Water00
1
A: Carbon monoxide dehydrogenase
B: Carbon monoxide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,28852
Polymers136,5762
Non-polymers6,71250
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Carbon monoxide dehydrogenase
D: Carbon monoxide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,84849
Polymers136,5762
Non-polymers6,27347
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.410, 230.050, 82.740
Angle α, β, γ (deg.)90.000, 101.520, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Carbon monoxide dehydrogenase


Mass: 68287.820 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901) (bacteria)
Strain: ATCC BAA-161 / DSM 6008 / Z-2901 / Gene: cooSV, CHY_0034 / Production host: Escherichia coli (E. coli)
References: UniProt: Q3AG28, anaerobic carbon monoxide dehydrogenase

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Non-polymers , 6 types, 97 molecules

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


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 61 / Source method: obtained synthetically / Formula: Xe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Br
#5: Chemical
ChemComp-T2N / 3,5-dioxa-7-thia-1-thionia-2$l^{2},4$l^{2},6$l^{3},8$l^{2}-tetraferrabicyclo[4.2.0]octane


Mass: 319.509 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4O2S2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H2S / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2

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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: 2.37 Å3/Da / Density % sol: 48.09 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris propane (pH 6.5), 0.15 M KSCN and 16-20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.9 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.9 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 83046 / % possible obs: 91.6 % / Redundancy: 3.8 % / CC1/2: 0.952 / Net I/σ(I): 14.7
Reflection shellResolution: 2.5→2.59 Å / Num. unique obs: 34051 / CC1/2: 0.929

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7B7Q

7b7q


Resolution: 2.5→20 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 27.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2758 4153 5 %
Rwork0.236 78893 -
obs0.238 83046 95.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 196.28 Å2 / Biso mean: 26.6662 Å2 / Biso min: 5.81 Å2
Refinement stepCycle: final / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19128 0 158 0 19286
Biso mean--48.16 --
Num. residues----2515
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.530.37121360.28582575271193
2.53-2.560.33551360.27442587272393
2.56-2.590.34151330.26142542267592
2.59-2.620.29941360.262569270594
2.62-2.660.3381350.27572570270592
2.66-2.690.38341290.31252467259690
2.69-2.730.27061350.24782569270494
2.73-2.770.26951390.23532637277693
2.77-2.810.27061360.24122584272095
2.81-2.860.32761360.25232577271394
2.86-2.910.30371390.25942657279696
2.91-2.960.24781360.25942583271994
2.96-3.020.30171420.25472685282796
3.02-3.080.30621350.24362577271295
3.08-3.150.2911400.24642648278896
3.15-3.220.28691380.23972632277095
3.22-3.30.27451410.23552667280896
3.3-3.390.26011370.23732618275596
3.39-3.490.32551360.26832577271392
3.49-3.60.26851400.24092663280396
3.6-3.730.30951360.24752567270393
3.73-3.880.26731400.22362656279696
3.88-4.050.29421360.24842584272094
4.05-4.260.20041420.20522690283298
4.26-4.530.2411420.19752705284798
4.53-4.870.2361440.20232729287398
4.87-5.350.23551430.20392725286899
5.35-6.110.25871430.21852716285998
6.11-7.630.23261450.21562762290799
7.63-200.24361470.20962775292299

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