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- PDB-8rc9: W-formate dehydrogenase from Desulfovibrio vulgaris - Co-crystall... -

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Basic information

Entry
Database: PDB / ID: 8rc9
TitleW-formate dehydrogenase from Desulfovibrio vulgaris - Co-crystallized with Formate and Exposed to air for 2 h
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 / OXYGEN MOLECULE / 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: 2.06 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)139,74115
Polymers136,2952
Non-polymers3,44613
Water3,729207
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9850 Å2
ΔGint-137 kcal/mol
Surface area38130 Å2
Unit cell
Length a, b, c (Å)65.180, 127.926, 149.467
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, 220 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
#4: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


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


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


Mass: 34.081 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2S
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.36 Å3/Da / Density % sol: 47.79 %
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 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.06→97.19 Å / Num. obs: 65092 / % possible obs: 87.87 % / Redundancy: 4.3 % / CC1/2: 0.991 / Net I/σ(I): 7
Reflection shellResolution: 2.06→2.15 Å / Num. unique obs: 3256 / CC1/2: 0.495

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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: 2.06→97.19 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 7.008 / SU ML: 0.179 / Cross valid method: FREE R-VALUE / ESU R: 0.294 / ESU R Free: 0.223
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2549 3244 4.984 %
Rwork0.2064 61843 -
all0.209 --
obs-65087 82.903 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 40.723 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å2-0 Å2
2---0.119 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.06→97.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9230 0 150 207 9587
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0139645
X-RAY DIFFRACTIONr_bond_other_d0.0010.0158903
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.6513127
X-RAY DIFFRACTIONr_angle_other_deg1.1531.58420556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.28751176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.64822.284486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.396151557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4961557
X-RAY DIFFRACTIONr_chiral_restr0.0660.21228
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210886
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022222
X-RAY DIFFRACTIONr_nbd_refined0.1940.21911
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.28502
X-RAY DIFFRACTIONr_nbtor_refined0.160.24549
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.24166
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2296
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0120.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1040.25
X-RAY DIFFRACTIONr_nbd_other0.1520.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3010.22
X-RAY DIFFRACTIONr_mcbond_it3.0984.2414716
X-RAY DIFFRACTIONr_mcbond_other3.0994.2414715
X-RAY DIFFRACTIONr_mcangle_it4.5656.3525888
X-RAY DIFFRACTIONr_mcangle_other4.5656.3525889
X-RAY DIFFRACTIONr_scbond_it2.8984.4044929
X-RAY DIFFRACTIONr_scbond_other2.8884.4074894
X-RAY DIFFRACTIONr_scangle_it4.3736.5097191
X-RAY DIFFRACTIONr_scangle_other4.3726.5127156
X-RAY DIFFRACTIONr_lrange_it6.16348.17210574
X-RAY DIFFRACTIONr_lrange_other6.15648.17610560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.1090.343550.3171124X-RAY DIFFRACTION20.5903
2.109-2.1670.3171630.2982877X-RAY DIFFRACTION54.0156
2.167-2.230.3182030.2853714X-RAY DIFFRACTION72.2694
2.23-2.2990.3162010.2683943X-RAY DIFFRACTION78.7533
2.299-2.3740.3052150.2464051X-RAY DIFFRACTION83.4507
2.374-2.4570.292310.2584241X-RAY DIFFRACTION89.9618
2.457-2.550.2882050.2344243X-RAY DIFFRACTION92.6474
2.55-2.6540.3041990.2494205X-RAY DIFFRACTION95.0983
2.654-2.7720.2992130.254081X-RAY DIFFRACTION96.5595
2.772-2.9070.3181980.253900X-RAY DIFFRACTION96.7879
2.907-3.0650.3111910.2483737X-RAY DIFFRACTION96.6298
3.065-3.250.2761920.2293517X-RAY DIFFRACTION96.3627
3.25-3.4750.2721920.2193276X-RAY DIFFRACTION96.0399
3.475-3.7530.2381670.2023066X-RAY DIFFRACTION95.8494
3.753-4.1110.2361520.1772833X-RAY DIFFRACTION95.5506
4.111-4.5960.1931520.1472551X-RAY DIFFRACTION95.0756
4.596-5.3060.1971040.1472265X-RAY DIFFRACTION93.9334
5.306-6.4960.229780.1611934X-RAY DIFFRACTION92.8044
6.496-9.1790.17810.1391463X-RAY DIFFRACTION90.7168
9.179-97.190.229520.186822X-RAY DIFFRACTION87.1386

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