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- PDB-9qm0: W-formate dehydrogenase U192C from Desulfovibrio vulgaris -

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Basic information

Entry
Database: PDB / ID: 9qm0
TitleW-formate dehydrogenase U192C from Desulfovibrio vulgaris
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 speciesNitratidesulfovibrio vulgaris str. Hildenborough (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.833 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)141,15033
Polymers136,2482
Non-polymers4,90231
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13880 Å2
ΔGint-85 kcal/mol
Surface area36530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.396, 123.099, 147.189
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 , 8 types, 462 molecules

#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#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-W / TUNGSTEN ION


Mass: 183.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: W / Feature type: SUBJECT OF INVESTIGATION
#8: 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
#9: 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
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 2.07 Å3/Da / Density % sol: 40.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 34% 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: 1.833→63.167 Å / Num. obs: 74505 / % possible obs: 92.92 % / Redundancy: 4.83 % / CC1/2: 0.9884 / Net I/σ(I): 5.959
Reflection shellResolution: 1.833→2.006 Å / Num. unique obs: 3725 / CC1/2: 0.668

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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 / Resolution: 1.833→63.167 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.121 / SU ML: 0.117 / Cross valid method: FREE R-VALUE / ESU R: 0.202 / ESU R Free: 0.165
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2135 3891 5.223 %
Rwork0.1723 70613 -
all0.175 --
obs-74504 74.387 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.248 Å2
Baniso -1Baniso -2Baniso -3
1-0.215 Å20 Å20 Å2
2---0.08 Å20 Å2
3----0.135 Å2
Refinement stepCycle: LAST / Resolution: 1.833→63.167 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9256 0 245 431 9932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0139762
X-RAY DIFFRACTIONr_bond_other_d0.0010.0159069
X-RAY DIFFRACTIONr_angle_refined_deg1.2621.65313239
X-RAY DIFFRACTIONr_angle_other_deg1.1461.58320937
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.88851186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.10822.301491
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.677151572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5791558
X-RAY DIFFRACTIONr_chiral_restr0.0560.21233
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210955
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022235
X-RAY DIFFRACTIONr_nbd_refined0.1860.21868
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1740.28803
X-RAY DIFFRACTIONr_nbtor_refined0.1580.24581
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.24234
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2446
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1280.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.140.28
X-RAY DIFFRACTIONr_nbd_other0.1760.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2080.210
X-RAY DIFFRACTIONr_mcbond_it3.2252.4394738
X-RAY DIFFRACTIONr_mcbond_other3.2222.4384737
X-RAY DIFFRACTIONr_mcangle_it4.1943.6525920
X-RAY DIFFRACTIONr_mcangle_other4.1943.6525921
X-RAY DIFFRACTIONr_scbond_it4.182.7715024
X-RAY DIFFRACTIONr_scbond_other4.1972.7794977
X-RAY DIFFRACTIONr_scangle_it5.7763.9817269
X-RAY DIFFRACTIONr_scangle_other5.7933.9887222
X-RAY DIFFRACTIONr_lrange_it6.77128.19810736
X-RAY DIFFRACTIONr_lrange_other6.76228.15110692
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.833-1.880.359120.273241X-RAY DIFFRACTION3.4653
1.88-1.9320.305390.252824X-RAY DIFFRACTION12.131
1.932-1.9880.296950.2441619X-RAY DIFFRACTION24.6903
1.988-2.0490.2811850.2393148X-RAY DIFFRACTION49.3632
2.049-2.1160.2562280.2274214X-RAY DIFFRACTION67.7961
2.116-2.1910.2622920.2255186X-RAY DIFFRACTION86.0374
2.191-2.2730.2562950.2135629X-RAY DIFFRACTION97.1307
2.273-2.3660.2632950.2035592X-RAY DIFFRACTION99.6108
2.366-2.4710.2452790.1985381X-RAY DIFFRACTION99.8412
2.471-2.5920.2362890.1815145X-RAY DIFFRACTION99.8346
2.592-2.7320.2262700.1744901X-RAY DIFFRACTION99.6915
2.732-2.8980.232490.1714590X-RAY DIFFRACTION99.3839
2.898-3.0980.2322390.1714367X-RAY DIFFRACTION99.4816
3.098-3.3460.2062250.1633981X-RAY DIFFRACTION97.723
3.346-3.6650.1782030.153617X-RAY DIFFRACTION95.3808
3.665-4.0970.1632020.1323399X-RAY DIFFRACTION99.6679
4.097-4.730.1411740.1243014X-RAY DIFFRACTION99.3766
4.73-5.7920.2051460.1572577X-RAY DIFFRACTION98.8385
5.792-8.1850.2071010.1632032X-RAY DIFFRACTION98.613
8.185-63.1670.22730.1771156X-RAY DIFFRACTION96.3922

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