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- PDB-30gj: W-formate dehydrogenase from Nitratidesulfovibrio vulgaris (Desul... -

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Basic information

Entry
Database: PDB / ID: 30gj
TitleW-formate dehydrogenase from Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris) - Ambient temperature, Serial crystallography
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 / electron transfer activity / periplasmic space / 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 speciesNitratidesulfovibrio vulgaris str. Hildenborough (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsVilela-Alves, G. / Martins, G. / von Stetten, D. / Mehrabi, P. / Pereira, I.C. / Romao, M.J. / Pearson, A.R. / 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 Tecnologiadoi.org/10.54499/2023.00286.BD Portugal
Fundacao para a Ciencia e a Tecnologiadoi.org/10.54499/UID/04378/2025 Portugal
Fundacao para a Ciencia e a Tecnologiadoi.org/10.54499/UID/PRR/04378/2025 Portugal
Fundacao para a Ciencia e a Tecnologiadoi.org/10.54499/LA/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: Acta Crystallogr D Struct Biol / Year: 2026
Title: Room-temperature crystal structure of a metal-dependent W-formate dehydrogenase by serial synchrotron crystallography.
Authors: Vilela-Alves, G. / Martins, G. / von Stetten, D. / Mehrabi, P. / Pereira, I.A.C. / Romao, M.J. / Pearson, A.R. / Mota, C.
History
DepositionApr 23, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2026Provider: 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)139,53210
Polymers136,4272
Non-polymers3,1068
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.500, 129.600, 151.900
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.) 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: 23989.508 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 , 5 types, 317 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.36 Å3/Da / Density % sol: 47.95 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 8 / Details: 32% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Mar 8, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.93→98.787 Å / Num. obs: 102629 / % possible obs: 100 % / Redundancy: 73.2 % / CC1/2: 0.9146 / CC star: 0.9775 / R split: 0.2854 / Net I/σ(I): 2.99
Reflection shellResolution: 1.93→2.01 Å / Redundancy: 50.3 % / Mean I/σ(I) obs: 1.02 / Num. unique obs: 10129 / CC1/2: 0.3768 / CC star: 0.7399 / R split: 1.0805 / % possible all: 100
Serial crystallography measurementPulse energy: 11.39 µJ / Source size: 100 µm2
Serial crystallography sample deliveryDescription: HARE chip / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: HARE chip
Sample dehydration prevention: Chamber at 95% relative humidity
Sample holding: HARE chip / Sample solvent: Mother liquor / Support base: HARE chip

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→98.787 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.048 / SU ML: 0.134 / Cross valid method: FREE R-VALUE / ESU R: 0.145 / ESU R Free: 0.135
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2224 5168 5.04 %
Rwork0.1849 97365 -
all0.187 --
obs-102533 99.996 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.871 Å2
Baniso -1Baniso -2Baniso -3
1-0.157 Å2-0 Å2-0 Å2
2---0.778 Å20 Å2
3---0.621 Å2
Refinement stepCycle: LAST / Resolution: 1.93→98.787 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9217 0 128 309 9654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0139624
X-RAY DIFFRACTIONr_bond_other_d0.0010.0158877
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.6513109
X-RAY DIFFRACTIONr_angle_other_deg1.2581.58420496
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.23751178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45822.305486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.009151558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0531557
X-RAY DIFFRACTIONr_chiral_restr0.0740.21227
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210899
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022225
X-RAY DIFFRACTIONr_nbd_refined0.2010.21636
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.27951
X-RAY DIFFRACTIONr_nbtor_refined0.1620.24598
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.24264
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2333
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0270.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0860.25
X-RAY DIFFRACTIONr_nbd_other0.220.227
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1840.22
X-RAY DIFFRACTIONr_mcbond_it1.9872.7784718
X-RAY DIFFRACTIONr_mcbond_other1.9872.7784717
X-RAY DIFFRACTIONr_mcangle_it3.0424.1615894
X-RAY DIFFRACTIONr_mcangle_other3.0424.1625895
X-RAY DIFFRACTIONr_scbond_it2.5133.0374906
X-RAY DIFFRACTIONr_scbond_other2.5183.0444871
X-RAY DIFFRACTIONr_scangle_it4.0434.4327167
X-RAY DIFFRACTIONr_scangle_other4.0514.4387132
X-RAY DIFFRACTIONr_lrange_it5.4231.38110362
X-RAY DIFFRACTIONr_lrange_other5.40931.35210327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.9490.3293960.317081X-RAY DIFFRACTION100
1.949-2.0030.3153730.36947X-RAY DIFFRACTION99.9863
2.003-2.0610.3013570.2766772X-RAY DIFFRACTION99.986
2.061-2.1240.2973450.2616572X-RAY DIFFRACTION100
2.124-2.1940.2873410.2436347X-RAY DIFFRACTION100
2.194-2.2710.2693370.2336163X-RAY DIFFRACTION100
2.271-2.3570.2643370.2155925X-RAY DIFFRACTION100
2.357-2.4530.2282770.2055747X-RAY DIFFRACTION100
2.453-2.5620.2292510.1935557X-RAY DIFFRACTION99.9828
2.562-2.6870.2682760.2015275X-RAY DIFFRACTION100
2.687-2.8320.2532720.1975028X-RAY DIFFRACTION100
2.832-3.0040.2072780.1854748X-RAY DIFFRACTION100
3.004-3.2110.2172490.1754452X-RAY DIFFRACTION100
3.211-3.4680.1932020.1574230X-RAY DIFFRACTION100
3.468-3.7990.182100.143866X-RAY DIFFRACTION100
3.799-4.2470.161940.1273503X-RAY DIFFRACTION100
4.247-4.9040.1591520.1183134X-RAY DIFFRACTION100
4.904-6.0040.1641410.1292681X-RAY DIFFRACTION100
6.004-8.4840.1921070.1392107X-RAY DIFFRACTION100
8.484-98.7870.159730.1581230X-RAY DIFFRACTION99.9233

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