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- PDB-6t7j: As-isolated Ni-free crystal structure of carbon monoxide dehydrog... -

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Basic information

Entry
Database: PDB / ID: 6t7j
TitleAs-isolated Ni-free crystal structure of carbon monoxide dehydrogenase from Thermococcus sp. AM4 produced without CooC maturase
ComponentsCarbon monoxide dehydrogenase
KeywordsOXIDOREDUCTASE / Ni-free cluster C / CO dehydrogenase
Function / homology
Function and homology information


: / anaerobic carbon monoxide dehydrogenase / anaerobic carbon-monoxide dehydrogenase activity / nickel cation binding / generation of precursor metabolites and energy / 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
(R,R)-2,3-BUTANEDIOL / CITRIC ACID / FE2/S2 (INORGANIC) CLUSTER / Broken Fe4S4 cluster / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / IRON/SULFUR CLUSTER / Carbon monoxide dehydrogenase
Similarity search - Component
Biological speciesThermococcus sp. AM4 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsDobbek, H. / Jeoung, J.-H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationEXC 2008/1 (UniSysCat) - 390540038 Germany
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2020
Title: The two CO-dehydrogenases of Thermococcus sp. AM4.
Authors: Benvenuti, M. / Meneghello, M. / Guendon, C. / Jacq-Bailly, A. / Jeoung, J.H. / Dobbek, H. / Leger, C. / Fourmond, V. / Dementin, S.
History
DepositionOct 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)208,09121
Polymers204,5053
Non-polymers3,58618
Water3,477193
1
B: Carbon monoxide dehydrogenase
hetero molecules

B: Carbon monoxide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,03818
Polymers136,3372
Non-polymers2,70116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area9350 Å2
ΔGint-118 kcal/mol
Surface area39080 Å2
MethodPISA
2
A: Carbon monoxide dehydrogenase
hetero molecules

D: Carbon monoxide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,57212
Polymers136,3372
Non-polymers2,23510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x+1/2,y+1/2,-z+11
Buried area9590 Å2
ΔGint-129 kcal/mol
Surface area37670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)268.138, 64.061, 100.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11D-851-

HOH

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Components

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Protein , 1 types, 3 molecules BAD

#1: Protein Carbon monoxide dehydrogenase


Mass: 68168.406 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: FS4)(FS4)(CX3)(PO4)(BU3)(BU3)(BU3)(PEG) are non-ploymers.
Source: (gene. exp.) Thermococcus sp. AM4 (archaea) / Gene: TAM4_1067 / Production host: Desulfovibrio fructosivorans (bacteria)
References: UniProt: B7R5K0, anaerobic carbon monoxide dehydrogenase

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Non-polymers , 8 types, 211 molecules

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


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical ChemComp-MSK / Broken Fe4S4 cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 41.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.1 M phosphate/citrate pH 4.2, 40% (w/v) polyethyleneglycol 300

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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, 1.732, 1.479
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91841
21.7321
31.4791
ReflectionResolution: 2.34→47.32 Å / Num. obs: 73992 / % possible obs: 99.3 % / Redundancy: 6.61 % / CC1/2: 0.997 / Net I/σ(I): 8.19
Reflection shellResolution: 2.34→2.48 Å / Num. unique obs: 11596 / CC1/2: 0.978

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Processing

Software
NameVersionClassification
PHENIX1.16-3549refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B53

3b53


Resolution: 2.43→47.32 Å / Cross valid method: FREE R-VALUE /
Num. reflection% reflection
obs73986 99.3 %
Displacement parametersBiso mean: 53.52 Å2
Refinement stepCycle: LAST / Resolution: 2.43→47.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14324 0 68 193 14585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008814690
X-RAY DIFFRACTIONf_angle_d0.874519977
X-RAY DIFFRACTIONf_chiral_restr0.04782296
X-RAY DIFFRACTIONf_plane_restr0.00412531
X-RAY DIFFRACTIONf_dihedral_angle_d20.56628910

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