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

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Basic information

Entry
Database: PDB / ID: 30gk
TitleW-formate dehydrogenase from Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris) - Same Batch SSX 2025/04/01
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 / 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: 1.953 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)140,96630
Polymers136,4272
Non-polymers4,53928
Water8,845491
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12890 Å2
ΔGint-102 kcal/mol
Surface area37800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.898, 127.884, 149.398
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 , 8 types, 519 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: C2H6O2
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / 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: 2.27 Å3/Da / Density % sol: 45.87 %
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: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Apr 1, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.953→59.524 Å / Num. obs: 89865 / % possible obs: 98.84 % / Redundancy: 13.11 % / Biso Wilson estimate: 29.18 Å2 / CC1/2: 0.9993 / Net I/σ(I): 18.801
Reflection shellResolution: 1.953→1.987 Å / Num. unique obs: 4440 / CC1/2: 0.739

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata processing
PHASERphasing
XDSdata reduction
Aimlessdata scaling
XSCALEdata scaling
pointlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.953→59.524 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.056 / SU ML: 0.138 / Cross valid method: FREE R-VALUE / ESU R: 0.198 / ESU R Free: 0.171
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.251 4482 4.987 %
Rwork0.2122 85383 -
all0.214 --
obs-89865 98.793 %
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: 39.827 Å2
Baniso -1Baniso -2Baniso -3
1-0.788 Å20 Å2-0 Å2
2---0.769 Å20 Å2
3----0.019 Å2
Refinement stepCycle: LAST / Resolution: 1.953→59.524 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9234 0 221 491 9946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0139716
X-RAY DIFFRACTIONr_bond_other_d0.0010.0159010
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.65313189
X-RAY DIFFRACTIONr_angle_other_deg1.0871.58320793
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.64951180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.55922.234488
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.689151560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5841558
X-RAY DIFFRACTIONr_chiral_restr0.0470.21229
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210912
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022230
X-RAY DIFFRACTIONr_nbd_refined0.1740.21944
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1710.28915
X-RAY DIFFRACTIONr_nbtor_refined0.1550.24590
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.24198
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2566
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0530.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1440.22
X-RAY DIFFRACTIONr_nbd_other0.1830.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0430.23
X-RAY DIFFRACTIONr_mcbond_it1.2194.1994723
X-RAY DIFFRACTIONr_mcbond_other1.2194.1994722
X-RAY DIFFRACTIONr_mcangle_it2.0756.2955899
X-RAY DIFFRACTIONr_mcangle_other2.0756.2955900
X-RAY DIFFRACTIONr_scbond_it1.0044.2664993
X-RAY DIFFRACTIONr_scbond_other1.0044.2664994
X-RAY DIFFRACTIONr_scangle_it1.7256.3397241
X-RAY DIFFRACTIONr_scangle_other1.7256.347242
X-RAY DIFFRACTIONr_lrange_it3.71448.18810945
X-RAY DIFFRACTIONr_lrange_other3.67148.09710863
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.953-2.0040.3243120.36205X-RAY DIFFRACTION98.0442
2.004-2.0590.3043070.2866064X-RAY DIFFRACTION98.3331
2.059-2.1180.3273190.285854X-RAY DIFFRACTION98.0464
2.118-2.1840.3373100.2745705X-RAY DIFFRACTION98.14
2.184-2.2550.3042930.2685551X-RAY DIFFRACTION98.3673
2.255-2.3340.2682670.2595433X-RAY DIFFRACTION98.5477
2.334-2.4220.2932920.2515168X-RAY DIFFRACTION98.7342
2.422-2.5210.2812580.2425052X-RAY DIFFRACTION98.8827
2.521-2.6330.2892460.2454836X-RAY DIFFRACTION99.0257
2.633-2.7620.2952560.2474646X-RAY DIFFRACTION99.1505
2.762-2.9110.2742440.2344423X-RAY DIFFRACTION99.2979
2.911-3.0880.2722180.2364178X-RAY DIFFRACTION98.8309
3.088-3.3010.2772020.2323945X-RAY DIFFRACTION99.4008
3.301-3.5650.2591930.223730X-RAY DIFFRACTION99.6697
3.565-3.9050.2261580.1913410X-RAY DIFFRACTION99.4426
3.905-4.3660.1821610.1573128X-RAY DIFFRACTION99.6667
4.366-5.0410.1721300.1512781X-RAY DIFFRACTION99.7601
5.041-6.1720.1971370.1532347X-RAY DIFFRACTION99.8392
6.172-8.7210.2061150.1431859X-RAY DIFFRACTION99.7473
8.721-59.5240.247640.1831069X-RAY DIFFRACTION97.6724

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