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- PDB-6dc2: Crystal structure of Desulfovibrio vulgaris carbon monoxide dehyd... -

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Basic information

Entry
Database: PDB / ID: 6dc2
TitleCrystal structure of Desulfovibrio vulgaris carbon monoxide dehydrogenase C301S variant
ComponentsCarbon monoxide dehydrogenase
KeywordsOXIDOREDUCTASE / nickel-iron-sulfur (Ni-Fe-S) cluster / iron-sulfur (Fe-S) cluster / metalloenzyme
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 / 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
: / FE2/S2 (INORGANIC) CLUSTER / IRON/SULFUR CLUSTER / FE(4)-NI(1)-S(4) CLUSTER / Carbon monoxide dehydrogenase
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.992 Å
AuthorsWittenborn, E.C. / Drennan, C.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM069857 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM008334 United States
CitationJournal: Elife / Year: 2018
Title: Redox-dependent rearrangements of the NiFeS cluster of carbon monoxide dehydrogenase.
Authors: Wittenborn, E.C. / Merrouch, M. / Ueda, C. / Fradale, L. / Leger, C. / Fourmond, V. / Pandelia, M.E. / Dementin, S. / Drennan, C.L.
History
DepositionMay 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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)274,91227
Polymers270,7994
Non-polymers4,11323
Water27,8511546
1
A: Carbon monoxide dehydrogenase
B: Carbon monoxide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,37613
Polymers135,4002
Non-polymers1,97611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10350 Å2
ΔGint-189 kcal/mol
Surface area36410 Å2
MethodPISA
2
C: Carbon monoxide dehydrogenase
D: Carbon monoxide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,53614
Polymers135,4002
Non-polymers2,13612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10820 Å2
ΔGint-186 kcal/mol
Surface area36040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.790, 144.150, 123.690
Angle α, β, γ (deg.)90.00, 98.50, 90.00
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: 67699.836 Da / Num. of mol.: 4 / Mutation: C301S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Gene: cooS, DVU_2098 / Production host: Desulfovibrio fructosivorans (bacteria)
References: UniProt: Q72A99, anaerobic carbon monoxide dehydrogenase

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Non-polymers , 7 types, 1569 molecules

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


Mass: 351.640 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Fe4S4
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical
ChemComp-XCC / FE(4)-NI(1)-S(4) CLUSTER / C CLUSTER


Mass: 410.333 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4NiS4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Fe
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1546 / Source method: isolated from a natural source / Formula: H2O

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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: 2.15 Å3/Da / Density % sol: 42.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 200 mM magnesium chloride, 18% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2017
RadiationMonochromator: Cryo-Cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.992→100 Å / Num. obs: 152978 / % possible obs: 97.9 % / Redundancy: 4.4 % / Rsym value: 0.155 / Net I/σ(I): 6.9
Reflection shellResolution: 1.992→2.04 Å / Num. unique obs: 41565 / Rsym value: 0.822

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6B6V

6b6v


Resolution: 1.992→93.272 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.67
RfactorNum. reflection% reflection
Rfree0.2119 7525 5.08 %
Rwork0.1632 --
obs0.1657 148102 96.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.992→93.272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18346 0 105 1546 19997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00518888
X-RAY DIFFRACTIONf_angle_d0.76525734
X-RAY DIFFRACTIONf_dihedral_angle_d23.5316910
X-RAY DIFFRACTIONf_chiral_restr0.073006
X-RAY DIFFRACTIONf_plane_restr0.0043375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.992-2.01460.40491300.33522507X-RAY DIFFRACTION52
2.0146-2.03830.30712580.25864771X-RAY DIFFRACTION99
2.0383-2.06320.3172550.23654810X-RAY DIFFRACTION99
2.0632-2.08930.26922600.22564840X-RAY DIFFRACTION100
2.0893-2.11680.28122540.22614721X-RAY DIFFRACTION99
2.1168-2.14580.31552500.22344824X-RAY DIFFRACTION99
2.1458-2.17640.29022600.21154801X-RAY DIFFRACTION99
2.1764-2.20890.26072550.19954754X-RAY DIFFRACTION99
2.2089-2.24340.25782700.19754776X-RAY DIFFRACTION99
2.2434-2.28020.25582510.19114682X-RAY DIFFRACTION98
2.2802-2.31950.26072420.19094738X-RAY DIFFRACTION97
2.3195-2.36170.23532470.17994705X-RAY DIFFRACTION98
2.3617-2.40710.23472430.17034848X-RAY DIFFRACTION100
2.4071-2.45630.23242530.16844792X-RAY DIFFRACTION100
2.4563-2.50970.23182650.16854847X-RAY DIFFRACTION100
2.5097-2.56810.22592620.16664766X-RAY DIFFRACTION99
2.5681-2.63230.22482850.16444777X-RAY DIFFRACTION99
2.6323-2.70350.22112620.16244799X-RAY DIFFRACTION99
2.7035-2.7830.24062550.16084776X-RAY DIFFRACTION99
2.783-2.87290.21512630.1644699X-RAY DIFFRACTION98
2.8729-2.97560.2212580.1624696X-RAY DIFFRACTION97
2.9756-3.09470.20452180.15584706X-RAY DIFFRACTION96
3.0947-3.23560.22272570.14964835X-RAY DIFFRACTION99
3.2356-3.40620.19062670.1454793X-RAY DIFFRACTION99
3.4062-3.61960.18152620.13594764X-RAY DIFFRACTION99
3.6196-3.8990.16612670.13574735X-RAY DIFFRACTION98
3.899-4.29140.14492370.12274703X-RAY DIFFRACTION96
4.2914-4.91240.14982310.12514660X-RAY DIFFRACTION96
4.9124-6.18890.17852710.15144747X-RAY DIFFRACTION98
6.1889-93.37480.18832370.16094705X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3460.087-0.01540.54250.08350.19790.0078-0.0308-0.07410.06740.01540.03590.0332-0.0308-0.02220.1573-0.0001-0.0220.1630.01730.201417.59582.134617.7758
20.30880.00430.06430.39330.00230.2269-0.0092-0.00380.08450.01740.0331-0.0449-0.02720.026-0.0230.1726-0.0046-0.01510.1882-0.01910.237935.750235.354911.097
30.30690.00010.01230.34510.03160.21290.0125-0.0203-0.0550.04140.02230.00840.0239-0.0523-0.0330.1753-0.0013-0.01820.21160.02520.2137-5.38874.765-42.2246
40.19930.00350.04990.6691-0.07120.25930.00110.00780.0512-0.00860.0219-0.1123-0.0410.002-0.02280.15340.0055-0.00280.163-0.00720.221612.916137.3779-51.2955
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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