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- PDB-6b6w: Crystal structure of Desulfovibrio vulgaris carbon monoxide dehyd... -

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Basic information

Entry
Database: PDB / ID: 6b6w
TitleCrystal structure of Desulfovibrio vulgaris carbon monoxide dehydrogenase, as-isolated (protein batch 2), oxidized C-cluster
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 / 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
Fe(4)-Ni(1)-S(4) cluster, oxidized / 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: 1.72 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
DepositionOct 3, 2017Deposition 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
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_alt_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.ptnr1_symmetry / _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_alt_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_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_symmetry

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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)138,48919
Polymers135,4322
Non-polymers3,05717
Water20,6631147
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11050 Å2
ΔGint-172 kcal/mol
Surface area36210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.430, 155.230, 66.570
Angle α, β, γ (deg.)90.00, 102.85, 90.00
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: 67715.898 Da / Num. of mol.: 2
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 , 8 types, 1164 molecules

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


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-XCC / FE(4)-NI(1)-S(4) CLUSTER / C CLUSTER


Mass: 410.333 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4NiS4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CUV / Fe(4)-Ni(1)-S(4) cluster, oxidized / C cluster, oxidized


Mass: 410.333 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4NiS4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1147 / 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: 2.4 Å3/Da / Density % sol: 48.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 150-250 mM magnesium chloride, 16-20% w/v 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-F / Detector: PIXEL / Date: Aug 7, 2016
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: 1.72→100 Å / Num. obs: 132968 / % possible obs: 98.7 % / Redundancy: 3.9 % / Rsym value: 0.078 / Net I/σ(I): 12
Reflection shellResolution: 1.72→1.75 Å / Rsym value: 0.542

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6B6V

6b6v


Resolution: 1.72→64.902 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.15
RfactorNum. reflection% reflection
Rfree0.1757 6633 4.99 %
Rwork0.1509 --
obs0.1521 132956 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.72→64.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9245 0 84 1147 10476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069933
X-RAY DIFFRACTIONf_angle_d1.07313612
X-RAY DIFFRACTIONf_dihedral_angle_d20.0026050
X-RAY DIFFRACTIONf_chiral_restr0.0461554
X-RAY DIFFRACTIONf_plane_restr0.0041787
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7201-1.73960.28491850.26373774X-RAY DIFFRACTION87
1.7396-1.76010.2622100.2483871X-RAY DIFFRACTION92
1.7601-1.78160.29682240.24244116X-RAY DIFFRACTION97
1.7816-1.80410.27322050.22214238X-RAY DIFFRACTION99
1.8041-1.82790.25232480.19944197X-RAY DIFFRACTION99
1.8279-1.85290.21542230.19314204X-RAY DIFFRACTION99
1.8529-1.87940.22812280.17844199X-RAY DIFFRACTION99
1.8794-1.90740.20042200.18864275X-RAY DIFFRACTION99
1.9074-1.93720.22642150.18544226X-RAY DIFFRACTION99
1.9372-1.9690.2092210.15794236X-RAY DIFFRACTION99
1.969-2.0030.17522270.15744227X-RAY DIFFRACTION100
2.003-2.03940.20121980.15654245X-RAY DIFFRACTION99
2.0394-2.07860.18552160.15564264X-RAY DIFFRACTION99
2.0786-2.1210.17062340.14934188X-RAY DIFFRACTION100
2.121-2.16720.19332310.14854261X-RAY DIFFRACTION100
2.1672-2.21760.17882240.15314293X-RAY DIFFRACTION100
2.2176-2.2730.20892200.16264193X-RAY DIFFRACTION99
2.273-2.33450.16172230.14264250X-RAY DIFFRACTION100
2.3345-2.40320.17452260.14254245X-RAY DIFFRACTION100
2.4032-2.48080.17532270.14164263X-RAY DIFFRACTION99
2.4808-2.56940.16892280.14274232X-RAY DIFFRACTION100
2.5694-2.67230.18992050.14754239X-RAY DIFFRACTION99
2.6723-2.79390.17112200.14384270X-RAY DIFFRACTION100
2.7939-2.94120.1612310.14514233X-RAY DIFFRACTION100
2.9412-3.12550.16392360.14584232X-RAY DIFFRACTION100
3.1255-3.36680.17482170.14524274X-RAY DIFFRACTION99
3.3668-3.70560.16492200.13694253X-RAY DIFFRACTION100
3.7056-4.24170.12742220.12274273X-RAY DIFFRACTION100
4.2417-5.34370.1522250.12214253X-RAY DIFFRACTION99
5.3437-64.94820.14362240.15434299X-RAY DIFFRACTION99
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)
10.356-0.1537-0.04210.8050.05280.45530.00090.0708-0.1271-0.08610.0318-0.030.10790.0238-0.0320.1175-0.0083-0.00760.1345-0.04630.133426.0252.124511.9734
20.3783-0.05180.01630.7239-0.11570.36470.01520.03860.0259-0.02570.04370.1051-0.0424-0.0785-0.04760.08610.0054-0.00080.12680.01780.09367.539335.65817.4712
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' )
2X-RAY DIFFRACTION2(chain 'B' )

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