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- PDB-7b7t: CooS-V with oxidized hybrid cluster -

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Basic information

Entry
Database: PDB / ID: 7b7t
TitleCooS-V with oxidized hybrid cluster
ComponentsCarbon monoxide dehydrogenase
KeywordsOXIDOREDUCTASE / Hybrid cluster / HCP / CODH
Function / homology
Function and homology information


anaerobic carbon monoxide dehydrogenase / anaerobic carbon-monoxide dehydrogenase activity / : / hydroxylamine reductase activity / nickel cation binding / generation of precursor metabolites and energy / response to hydrogen peroxide / 2 iron, 2 sulfur cluster binding / peroxidase activity / 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
(R,R)-2,3-BUTANEDIOL / FE2/S2 (INORGANIC) CLUSTER / DI(HYDROXYETHYL)ETHER / FE4-S3 CLUSTER / IRON/SULFUR CLUSTER / Carbon monoxide dehydrogenase
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 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

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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)138,39610
Polymers136,5762
Non-polymers1,8218
Water24,4281356
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10450 Å2
ΔGint-153 kcal/mol
Surface area36270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.768, 107.796, 82.093
Angle α, β, γ (deg.)90.000, 98.660, 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: 68287.820 Da / Num. of mol.: 2
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, 1364 molecules

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


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#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-SF3 / FE4-S3 CLUSTER


Mass: 319.575 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#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.: 1356 / 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: 41.61 %
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: 1.38→47.383 Å / Num. obs: 228651 / % possible obs: 98.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 14.16 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.8
Reflection shellResolution: 1.38→1.43 Å / Num. unique obs: 22516 / CC1/2: 0.599 / % possible all: 97.4

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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: 7B7Q

7b7q


Resolution: 1.38→47.383 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 16.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1597 2401 1.05 %
Rwork0.131 226246 -
obs0.1314 228647 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.81 Å2 / Biso mean: 21.8703 Å2 / Biso min: 8.66 Å2
Refinement stepCycle: final / Resolution: 1.38→47.383 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9568 0 84 1356 11008
Biso mean--31.52 34.27 -
Num. residues----1258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01210245
X-RAY DIFFRACTIONf_angle_d1.41314016
X-RAY DIFFRACTIONf_chiral_restr0.0881632
X-RAY DIFFRACTIONf_plane_restr0.0081807
X-RAY DIFFRACTIONf_dihedral_angle_d18.7193967
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.38-1.40820.28361390.2271315698
1.4082-1.43880.22831390.21521304897
1.4388-1.47230.24811400.18331322498
1.4723-1.50910.23221400.16181322099
1.5091-1.54990.19071410.14771326099
1.5499-1.59550.19731410.13351331399
1.5955-1.6470.1721410.12491327899
1.647-1.70590.15751400.11941313198
1.7059-1.77420.15961410.11321336399
1.7742-1.85490.15091420.10921331899
1.8549-1.95270.15111420.11011341599
1.9527-2.07510.14541420.112213397100
2.0751-2.23530.13941410.11221325399
2.2353-2.46020.1371430.114213487100
2.4602-2.81620.14271430.125713469100
2.8162-3.54790.14061410.13681334299
3.5479-47.3830.16721450.13961357299

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