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- PDB-8rc8: W-formate dehydrogenase from Desulfovibrio vulgaris - Co-crystall... -

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Basic information

Entry
Database: PDB / ID: 8rc8
TitleW-formate dehydrogenase from Desulfovibrio vulgaris - Co-crystallized with Formate and Exposed to air for 0 min
Components(Formate dehydrogenase, ...) x 2
KeywordsOXIDOREDUCTASE / Formate / CO2 / Molybdenum and Tungsten enzymes / DMSO reductase family / ELECTRON TRANSPORT
Function / homology
Function and homology information


formate dehydrogenase (cytochrome-c-553) activity / formate dehydrogenase / formate dehydrogenase (NAD+) activity / molybdenum ion binding / molybdopterin cofactor binding / anaerobic respiration / cell envelope / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / metal ion binding
Similarity search - Function
Formate dehydrogenase-N, alpha subunit / : / 4Fe-4S dicluster domain / Molybdopterin oxidoreductase, molybdopterin cofactor binding site / Prokaryotic molybdopterin oxidoreductases signature 1. / Prokaryotic molybdopterin oxidoreductases signature 3. / Molybdopterin oxidoreductase, prokaryotic, conserved site / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain ...Formate dehydrogenase-N, alpha subunit / : / 4Fe-4S dicluster domain / Molybdopterin oxidoreductase, molybdopterin cofactor binding site / Prokaryotic molybdopterin oxidoreductases signature 1. / Prokaryotic molybdopterin oxidoreductases signature 3. / Molybdopterin oxidoreductase, prokaryotic, conserved site / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
HYDROSULFURIC ACID / Chem-MGD / DI(HYDROXYETHYL)ETHER / IRON/SULFUR CLUSTER / : / Formate dehydrogenase, beta subunit, putative / Formate dehydrogenase, alpha subunit, selenocysteine-containing
Similarity search - Component
Biological speciesDesulfovibrio vulgaris str. Hildenborough (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.005 Å
AuthorsVilela-Alves, G. / Manuel, R.R. / Pereira, I.C. / Romao, M.J. / Mota, C.
Funding support Portugal, 8items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPTDC/BII-BBF/2050/2020 Portugal
Fundacao para a Ciencia e a TecnologiaUIDP/04378/2020 Portugal
Fundacao para a Ciencia e a TecnologiaUIDB/04378/2020 Portugal
Fundacao para a Ciencia e a TecnologiaUIDB/04612/2020 Portugal
Fundacao para a Ciencia e a TecnologiaUIDP/04612/2020 Portugal
Fundacao para a Ciencia e a TecnologiaLA/P/0140/2020 Portugal
Fundacao para a Ciencia e a TecnologiaLA/P/0087/2020 Portugal
Fundacao para a Ciencia e a Tecnologia2023.00286.BD Portugal
CitationJournal: Chem Sci / Year: 2024
Title: Substrate-dependent oxidative inactivation of a W-dependent formate dehydrogenase involving selenocysteine displacement.
Authors: Vilela-Alves, G. / Manuel, R.R. / Viegas, A. / Carpentier, P. / Biaso, F. / Guigliarelli, B. / Pereira, I.A.C. / Romao, M.J. / Mota, C.
History
DepositionDec 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._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_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 23, 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: Formate dehydrogenase, alpha subunit, selenocysteine-containing
B: Formate dehydrogenase, beta subunit, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,06218
Polymers136,2952
Non-polymers3,76616
Water7,602422
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10530 Å2
ΔGint-135 kcal/mol
Surface area37890 Å2
Unit cell
Length a, b, c (Å)64.988, 124.345, 149.899
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Formate dehydrogenase, ... , 2 types, 2 molecules AB

#1: Protein Formate dehydrogenase, alpha subunit, selenocysteine-containing


Mass: 112437.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris str. Hildenborough (bacteria)
Strain: Hildenborough / Gene: fdnG-1, DVU_0587
Production host: Desulfovibrio vulgaris str. Hildenborough (bacteria)
Strain (production host): Hildenborough / References: UniProt: Q72EJ1, formate dehydrogenase
#2: Protein Formate dehydrogenase, beta subunit, putative


Mass: 23858.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris str. Hildenborough (bacteria)
Strain: Hildenborough / Gene: DVU_0588
Production host: Desulfovibrio vulgaris str. Hildenborough (bacteria)
Strain (production host): Hildenborough / References: UniProt: Q72EJ0

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Non-polymers , 8 types, 438 molecules

#3: Chemical ChemComp-MGD / 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE / MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE


Mass: 740.557 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-W / TUNGSTEN ION


Mass: 183.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: W / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2S / Feature type: SUBJECT OF INVESTIGATION
#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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / 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: 2.22 Å3/Da / Density % sol: 44.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 22% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2→47.898 Å / Num. obs: 82099 / % possible obs: 99.6 % / Redundancy: 7 % / CC1/2: 0.994 / Net I/σ(I): 6.6
Reflection shellResolution: 2→2.04 Å / Num. unique obs: 4138 / CC1/2: 0.527

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
autoPROCdata processing
Aimlessdata scaling
PHASERphasing
XDSdata reduction
Aimlessdata scaling
XSCALEdata scaling
pointlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SDV

6sdv


Resolution: 2.005→47.898 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.789 / SU ML: 0.125 / Cross valid method: FREE R-VALUE / ESU R: 0.186 / ESU R Free: 0.159
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2195 4152 5.063 %
Rwork0.1811 77848 -
all0.183 --
obs-82000 99.706 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.3 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 31.242 Å2
Baniso -1Baniso -2Baniso -3
1-0.796 Å2-0 Å20 Å2
2---1.28 Å20 Å2
3---0.484 Å2
Refinement stepCycle: LAST / Resolution: 2.005→47.898 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9211 0 171 422 9804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0129644
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168613
X-RAY DIFFRACTIONr_angle_refined_deg1.0521.65413117
X-RAY DIFFRACTIONr_angle_other_deg0.3621.56620125
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.72451175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.388559
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.971101555
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.14510426
X-RAY DIFFRACTIONr_chiral_restr0.0580.21388
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210900
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021918
X-RAY DIFFRACTIONr_nbd_refined0.20.21765
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.27921
X-RAY DIFFRACTIONr_nbtor_refined0.1710.24626
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.24660
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2377
X-RAY DIFFRACTIONr_metal_ion_refined0.0810.214
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2430.212
X-RAY DIFFRACTIONr_nbd_other0.2080.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1510.23
X-RAY DIFFRACTIONr_mcbond_it2.8733.1684709
X-RAY DIFFRACTIONr_mcbond_other2.8723.1684709
X-RAY DIFFRACTIONr_mcangle_it3.9694.7395881
X-RAY DIFFRACTIONr_mcangle_other3.9684.7395882
X-RAY DIFFRACTIONr_scbond_it3.2863.4124935
X-RAY DIFFRACTIONr_scbond_other3.2863.4124936
X-RAY DIFFRACTIONr_scangle_it4.7744.9867188
X-RAY DIFFRACTIONr_scangle_other4.7734.9867189
X-RAY DIFFRACTIONr_lrange_it6.539.27410661
X-RAY DIFFRACTIONr_lrange_other6.42438.93410603
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.005-2.0570.3432970.30755150.30959930.9220.93696.97980.309
2.057-2.1130.32740.27355630.27458370.9450.9491000.275
2.113-2.1740.2462950.24753970.24756920.9580.9581000.248
2.174-2.2410.2682510.23352920.23455430.950.9631000.231
2.241-2.3140.2412740.20950750.21153490.960.9711000.205
2.314-2.3950.2392590.249370.20251960.9640.9731000.195
2.395-2.4860.2412810.19347440.19550250.9590.9751000.185
2.486-2.5870.2662460.19145820.19548280.9520.9761000.183
2.587-2.7020.1992300.17344340.17446650.9760.98199.97860.166
2.702-2.8330.2282200.17642170.17944380.970.98199.97750.169
2.833-2.9860.2242220.17340160.17542380.9690.9821000.165
2.986-3.1660.2171960.17138250.17340220.970.98399.97510.163
3.166-3.3830.2331940.17335910.17637870.9660.98299.94720.166
3.383-3.6530.1931910.17333570.17435490.9760.98399.97180.167
3.653-3.9990.2041740.15830870.16132630.9780.98699.93870.154
3.999-4.4680.171440.13928200.1429680.9840.98999.86520.137
4.468-5.1510.1771240.13925280.14126550.9820.98999.8870.137
5.151-6.2910.1951280.16221400.16422700.9840.98899.91190.16
6.291-8.8210.205990.16816940.1717970.9820.98799.77740.167
8.821-47.8980.203530.18810320.18910900.9790.98399.54130.21

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