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- PDB-7b7q: CooS-V with oxidized hybrid cluster -

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Basic information

Entry
Database: PDB / ID: 7b7q
TitleCooS-V with oxidized hybrid cluster
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
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 / Chem-T2N / Carbon monoxide dehydrogenase
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsJeoung, J.H. / Dobbek, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)390540038 Germany
CitationJournal: 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.
History
DepositionDec 11, 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
Revision 1.3Nov 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
A: Carbon monoxide dehydrogenase
B: Carbon monoxide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,53310
Polymers136,6402
Non-polymers1,8948
Water23,1671286
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9910 Å2
ΔGint-98 kcal/mol
Surface area36840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.327, 108.982, 82.843
Angle α, β, γ (deg.)90.000, 98.780, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Carbon monoxide dehydrogenase


Mass: 68319.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CSS is S-MERCAPTOCYSTEINE.
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, 1294 molecules

#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#4: 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.: 2 / Source method: obtained synthetically / Formula: Fe4O2S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1286 / 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: 2.17 Å3/Da / Density % sol: 43.2 %
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: 0.9184 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: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.35→45.362 Å / Num. obs: 251838 / % possible obs: 99.06 % / Redundancy: 5.1 % / Biso Wilson estimate: 17.5 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.1
Reflection shellResolution: 1.35→1.4 Å / Num. unique obs: 251838 / CC1/2: 0.999

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B53

3b53


Resolution: 1.35→45.362 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1579 2644 1.05 %
Rwork0.1331 249178 -
obs0.1334 251822 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.66 Å2 / Biso mean: 26.4203 Å2 / Biso min: 12.33 Å2
Refinement stepCycle: final / Resolution: 1.35→45.362 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9570 0 98 1286 10954
Biso mean--45 37.43 -
Num. residues----1258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110106
X-RAY DIFFRACTIONf_angle_d1.11113783
X-RAY DIFFRACTIONf_chiral_restr0.0961602
X-RAY DIFFRACTIONf_plane_restr0.0081776
X-RAY DIFFRACTIONf_dihedral_angle_d19.6723863
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.35-1.37450.30841390.26931310399
1.3745-1.4010.25021400.23261312299
1.401-1.42960.24281380.21191307699
1.4296-1.46070.2451390.19631303099
1.4607-1.49470.21911380.17571301199
1.4947-1.5320.19111380.14941302798
1.532-1.57350.1681390.13521307899
1.5735-1.61980.15161390.12081313199
1.6198-1.6720.16211390.11451310999
1.672-1.73180.1511390.11291312799
1.7318-1.80110.16321400.11371312099
1.8011-1.88310.13971380.11461302899
1.8831-1.98240.15941380.121304099
1.9824-2.10660.1431400.12413214100
2.1066-2.26930.14821410.122713227100
2.2693-2.49760.14561390.12481312099
2.4976-2.8590.15441390.13111305898
2.859-3.60180.16541400.135313264100
3.6018-45.3620.14061410.13321329399

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