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

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Basic information

Entry
Database: PDB / ID: 8rca
TitleW-formate dehydrogenase from Desulfovibrio vulgaris - Co-crystallized with Formate and Reoxidized by exposure to air for 1 h in the absence of Formate
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 / molybdopterin cofactor binding / cellular respiration / 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 / 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: 1.664 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

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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)140,01617
Polymers136,2952
Non-polymers3,72015
Water10,251569
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10440 Å2
ΔGint-143 kcal/mol
Surface area37700 Å2
Unit cell
Length a, b, c (Å)64.558, 128.006, 148.905
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 , 7 types, 584 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-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-W / TUNGSTEN ION


Mass: 183.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: W / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 569 / 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: 2.26 Å3/Da / Density % sol: 45.51 %
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: ID23-1 / Wavelength: 0.7749 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Dec 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.664→97.258 Å / Num. obs: 108396 / % possible obs: 90.6 % / Redundancy: 4.66 % / CC1/2: 0.9956 / Net I/σ(I): 7.992
Reflection shellResolution: 1.664→1.792 Å / Num. unique obs: 5420 / CC1/2: 0.6281

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata processing
STARANISOdata scaling
PHASERphasing
XDSdata reduction
Aimlessdata scaling
XSCALEdata scaling
pointlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SDV

6sdv


Resolution: 1.664→97.258 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.321 / SU ML: 0.103 / Cross valid method: FREE R-VALUE / ESU R: 0.144 / ESU R Free: 0.135
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2322 5448 5.026 %
Rwork0.1939 102948 -
all0.196 --
obs-108396 74.709 %
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: 30.649 Å2
Baniso -1Baniso -2Baniso -3
1-0.321 Å20 Å2-0 Å2
2---0.25 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.664→97.258 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9234 0 168 569 9971
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0139666
X-RAY DIFFRACTIONr_bond_other_d0.0010.0158923
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.6513153
X-RAY DIFFRACTIONr_angle_other_deg1.2691.58420604
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.34251178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36522.284486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.003151557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7531557
X-RAY DIFFRACTIONr_chiral_restr0.0790.21228
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210900
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022224
X-RAY DIFFRACTIONr_nbd_refined0.2040.21991
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.28866
X-RAY DIFFRACTIONr_nbtor_refined0.1650.24642
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.24296
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2536
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0520.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0960.29
X-RAY DIFFRACTIONr_nbd_other0.1840.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1620.23
X-RAY DIFFRACTIONr_mcbond_it2.2353.1224721
X-RAY DIFFRACTIONr_mcbond_other2.2353.1224720
X-RAY DIFFRACTIONr_mcangle_it3.1964.6785896
X-RAY DIFFRACTIONr_mcangle_other3.1964.6785897
X-RAY DIFFRACTIONr_scbond_it2.4523.3084945
X-RAY DIFFRACTIONr_scbond_other2.4523.3084946
X-RAY DIFFRACTIONr_scangle_it3.7544.8657209
X-RAY DIFFRACTIONr_scangle_other3.7544.8647210
X-RAY DIFFRACTIONr_lrange_it5.00936.24510966
X-RAY DIFFRACTIONr_lrange_other4.97536.15310884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.664-1.7070.291180.269423X-RAY DIFFRACTION4.1447
1.707-1.7540.288790.2791833X-RAY DIFFRACTION18.4609
1.754-1.8050.2822060.284086X-RAY DIFFRACTION42.749
1.805-1.860.3183180.2695697X-RAY DIFFRACTION61.3525
1.86-1.9210.2893420.2586412X-RAY DIFFRACTION71.3727
1.921-1.9880.2843510.2536751X-RAY DIFFRACTION77.0449
1.988-2.0640.2743790.2467197X-RAY DIFFRACTION85.5079
2.064-2.1480.3014100.2377575X-RAY DIFFRACTION93.0544
2.148-2.2430.2914040.2367645X-RAY DIFFRACTION97.9912
2.243-2.3530.2653940.2257361X-RAY DIFFRACTION98.8402
2.353-2.480.263700.2196956X-RAY DIFFRACTION97.4461
2.48-2.630.2613300.2096521X-RAY DIFFRACTION97.0947
2.63-2.8120.2683140.1986202X-RAY DIFFRACTION96.849
2.812-3.0370.2493470.2055749X-RAY DIFFRACTION98.0537
3.037-3.3270.2352810.1965354X-RAY DIFFRACTION97.8129
3.327-3.7190.2062630.1864832X-RAY DIFFRACTION97.3629
3.719-4.2940.1722380.1414285X-RAY DIFFRACTION96.873
4.294-5.2580.1581800.1293558X-RAY DIFFRACTION94.9695
5.258-7.4320.21440.1572873X-RAY DIFFRACTION96.544
7.432-97.2580.173800.1561638X-RAY DIFFRACTION94.137

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