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- PDB-9qm1: W-formate dehydrogenase U192C from Desulfovibrio vulgaris - Soake... -

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Basic information

Entry
Database: PDB / ID: 9qm1
TitleW-formate dehydrogenase U192C from Desulfovibrio vulgaris - Soaked with Dithionite
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 / cell envelope / anaerobic 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 / DI(HYDROXYETHYL)ETHER / IRON/SULFUR CLUSTER / SULFUR DIOXIDE / : / Formate dehydrogenase, beta subunit, putative / Formate dehydrogenase, alpha subunit, selenocysteine-containing
Similarity search - Component
Biological speciesNitratidesulfovibrio vulgaris str. Hildenborough (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.997 Å
AuthorsVilela-Alves, G. / Oliveira, A.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 Tecnologia2023.00286.BD 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 TecnologiaLA/P/0140/2020 Portugal
Fundacao para a Ciencia e a TecnologiaLA/P/0087/2020 Portugal
Fundacao para a Ciencia e a TecnologiaUIDB/04612/2020 Portugal
Fundacao para a Ciencia e a TecnologiaUIDP/04612/2020 Portugal
CitationJournal: Acs Catalysis / Year: 2025
Title: The Role of Selenocysteine in Catalysis and Oxygen Tolerance of a W‐Dependent Formate Dehydrogenase
Authors: Oliveira, A.R. / Vilela-Alves, G. / Mota, C. / Fourmond, V. / Leger, C. / Biaso, F. / Guigliarelli, B. / Romao, M.J. / Pereira, I.C.
History
DepositionMar 21, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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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)140,01919
Polymers136,2482
Non-polymers3,77017
Water7,476415
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10600 Å2
ΔGint-128 kcal/mol
Surface area36290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.800, 122.511, 146.697
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: 112390.133 Da / Num. of mol.: 1 / Mutation: U192C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitratidesulfovibrio vulgaris str. Hildenborough (bacteria)
Strain: Hildenborough / Gene: fdnG-1, DVU_0587
Production host: Nitratidesulfovibrio 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.) Nitratidesulfovibrio vulgaris str. Hildenborough (bacteria)
Strain: Hildenborough / Gene: DVU_0588
Production host: Nitratidesulfovibrio vulgaris str. Hildenborough (bacteria)
Strain (production host): Hildenborough / References: UniProt: Q72EJ0

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Non-polymers , 9 types, 432 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-SO2 / SULFUR DIOXIDE


Mass: 64.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2S / Feature type: SUBJECT OF INVESTIGATION
#7: 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
#8: Chemical ChemComp-W / TUNGSTEN ION


Mass: 183.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: W / Feature type: SUBJECT OF INVESTIGATION
#9: 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
#10: 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
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.04 Å3/Da / Density % sol: 39.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 26% 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: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jun 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.997→62.93 Å / Num. obs: 76000 / % possible obs: 99.57 % / Redundancy: 7 % / CC1/2: 0.994 / Net I/σ(I): 9.3
Reflection shellResolution: 1.997→2.03 Å / Num. unique obs: 3736 / CC1/2: 0.682

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.997→62.93 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.897 / SU B: 6.359 / SU ML: 0.169 / Cross valid method: FREE R-VALUE / ESU R: 0.237 / ESU R Free: 0.2
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2672 3696 4.863 %
Rwork0.2139 72304 -
all0.216 --
obs-76000 99.534 %
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.3 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 31.133 Å2
Baniso -1Baniso -2Baniso -3
1-1.038 Å20 Å2-0 Å2
2---0.928 Å20 Å2
3----0.111 Å2
Refinement stepCycle: LAST / Resolution: 1.997→62.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9235 0 170 415 9820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0139672
X-RAY DIFFRACTIONr_bond_other_d0.0010.0158954
X-RAY DIFFRACTIONr_angle_refined_deg1.2381.65113151
X-RAY DIFFRACTIONr_angle_other_deg1.0791.58420672
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.81351180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5322.254488
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.718151568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1891558
X-RAY DIFFRACTIONr_chiral_restr0.0470.21230
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210906
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022228
X-RAY DIFFRACTIONr_nbd_refined0.1760.21965
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.29134
X-RAY DIFFRACTIONr_nbtor_refined0.1560.24545
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.24310
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2486
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0460.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0730.27
X-RAY DIFFRACTIONr_nbd_other0.1640.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1220.26
X-RAY DIFFRACTIONr_mcbond_it11.8593.0824723
X-RAY DIFFRACTIONr_mcbond_other11.8593.0824722
X-RAY DIFFRACTIONr_mcangle_it12.6634.5995899
X-RAY DIFFRACTIONr_mcangle_other12.6624.5995900
X-RAY DIFFRACTIONr_scbond_it12.2023.3894949
X-RAY DIFFRACTIONr_scbond_other12.2593.4044902
X-RAY DIFFRACTIONr_scangle_it13.5294.8967203
X-RAY DIFFRACTIONr_scangle_other13.5724.917156
X-RAY DIFFRACTIONr_lrange_it14.91935.67610836
X-RAY DIFFRACTIONr_lrange_other14.94535.63910785
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.997-2.0490.3672850.2945281X-RAY DIFFRACTION99.982
2.049-2.1050.3532590.2845167X-RAY DIFFRACTION100
2.105-2.1660.3382480.2695003X-RAY DIFFRACTION99.9619
2.166-2.2330.3072520.2714924X-RAY DIFFRACTION100
2.233-2.3060.3242230.2544753X-RAY DIFFRACTION99.9197
2.306-2.3870.322480.2554574X-RAY DIFFRACTION99.7311
2.387-2.4770.2912230.2454434X-RAY DIFFRACTION99.9142
2.477-2.5780.2932260.2344266X-RAY DIFFRACTION99.623
2.578-2.6930.3352070.2464078X-RAY DIFFRACTION99.2587
2.693-2.8240.291910.2243915X-RAY DIFFRACTION99.6602
2.824-2.9770.2721940.2153730X-RAY DIFFRACTION99.7205
2.977-3.1580.2841780.2143540X-RAY DIFFRACTION99.5182
3.158-3.3760.2341510.1953268X-RAY DIFFRACTION97.1859
3.376-3.6460.2471570.1963036X-RAY DIFFRACTION96.9044
3.646-3.9940.2321580.1792880X-RAY DIFFRACTION99.9671
3.994-4.4650.1981460.152630X-RAY DIFFRACTION99.964
4.465-5.1540.2121110.1582347X-RAY DIFFRACTION100
5.154-6.3110.1751060.171986X-RAY DIFFRACTION100
6.311-8.9170.217880.1771565X-RAY DIFFRACTION99.8188
8.917-62.930.31450.236927X-RAY DIFFRACTION98.881

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