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- PDB-9rjt: W-formate dehydrogenase from Nitratidesulfovibrio vulgaris (Desul... -

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Basic information

Entry
Database: PDB / ID: 9rjt
TitleW-formate dehydrogenase from Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris) - Dithionite reduced - anaerobic soaked with 58 bar CO2 for 1 min
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
CARBON DIOXIDE / 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: 1.83 Å
AuthorsVilela-Alves, G. / Manuel, R.R. / Carpentier, P. / Pereira, I.C. / Romao, M.J. / Mota, C.
Funding support Portugal, 7items
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 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: Angew.Chem.Int.Ed.Engl. / Year: 2026
Title: Structural Insights into CO2 Transport Pathways in a W-Formate Dehydrogenase: Structural Basis for CO2 Reduction
Authors: Vilela-Alves, G. / Manuel, R.R. / Martins, G. / Carpentier, P. / Pereira, I.C. / Romao, M.J. / Mota, C.
History
DepositionJun 12, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 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)141,00739
Polymers136,4272
Non-polymers4,58037
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13770 Å2
ΔGint-138 kcal/mol
Surface area37060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.993, 124.845, 150.480
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)
Gene: fdnG-1, DVU_0587
Production host: Desulfovibrio vulgaris str. Hildenborough (bacteria)
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: Desulfovibrio vulgaris str. Hildenborough (bacteria)
References: UniProt: Q72EJ0

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Non-polymers , 8 types, 360 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-W / TUNGSTEN ION


Mass: 183.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: W / Feature type: SUBJECT OF INVESTIGATION
#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-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: CO2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.24 Å3/Da / Density % sol: 45.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / 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: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.83→64.442 Å / Num. obs: 73531 / % possible obs: 88.57 % / Redundancy: 8.53 % / CC1/2: 0.9887 / Net I/σ(I): 8.518
Reflection shellResolution: 1.83→1.988 Å / Num. unique obs: 3677 / CC1/2: 0.4894

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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: 1.83→64.442 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.908 / SU B: 4.421 / SU ML: 0.128 / Cross valid method: FREE R-VALUE / ESU R: 0.228 / ESU R Free: 0.191
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2405 3726 5.072 %
Rwork0.1902 69742 -
all0.193 --
obs-73468 67.649 %
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: 23.749 Å2
Baniso -1Baniso -2Baniso -3
1-0.072 Å20 Å20 Å2
2--0.002 Å2-0 Å2
3----0.075 Å2
Refinement stepCycle: LAST / Resolution: 1.83→64.442 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9213 0 227 323 9763
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0139693
X-RAY DIFFRACTIONr_bond_other_d0.0010.0158915
X-RAY DIFFRACTIONr_angle_refined_deg1.3741.65313154
X-RAY DIFFRACTIONr_angle_other_deg1.1881.58420579
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.17451179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49822.305486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.832151558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0461557
X-RAY DIFFRACTIONr_chiral_restr0.0660.21227
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210908
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022224
X-RAY DIFFRACTIONr_nbd_refined0.1950.21998
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.28659
X-RAY DIFFRACTIONr_nbtor_refined0.1610.24612
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.24248
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2402
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0640.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2360.29
X-RAY DIFFRACTIONr_nbd_other0.1750.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1120.23
X-RAY DIFFRACTIONr_mcbond_it2.662.3454713
X-RAY DIFFRACTIONr_mcbond_other2.6592.3454712
X-RAY DIFFRACTIONr_mcangle_it3.8783.5115887
X-RAY DIFFRACTIONr_mcangle_other3.8793.5115888
X-RAY DIFFRACTIONr_scbond_it3.1892.6234980
X-RAY DIFFRACTIONr_scbond_other3.182.6214971
X-RAY DIFFRACTIONr_scangle_it4.7753.7937217
X-RAY DIFFRACTIONr_scangle_other4.773.7927213
X-RAY DIFFRACTIONr_lrange_it6.40627.2610803
X-RAY DIFFRACTIONr_lrange_other6.38827.23710754
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.8770.247140.291236X-RAY DIFFRACTION3.1324
1.877-1.9290.319690.291127X-RAY DIFFRACTION15.4682
1.929-1.9850.31980.2842019X-RAY DIFFRACTION28.1591
1.985-2.0460.2721500.2622736X-RAY DIFFRACTION39.3456
2.046-2.1130.3011860.2523361X-RAY DIFFRACTION50.1981
2.113-2.1870.2821910.2443762X-RAY DIFFRACTION57.423
2.187-2.270.2882180.2434623X-RAY DIFFRACTION72.9946
2.27-2.3620.2752670.2415303X-RAY DIFFRACTION87.0449
2.362-2.4670.2722960.2215547X-RAY DIFFRACTION94.6695
2.467-2.5880.2562870.2175459X-RAY DIFFRACTION98.0379
2.588-2.7280.2462880.2085235X-RAY DIFFRACTION98.0124
2.728-2.8930.2742740.2014888X-RAY DIFFRACTION97.6911
2.893-3.0930.2562510.2024400X-RAY DIFFRACTION92.6679
3.093-3.340.2192050.1793631X-RAY DIFFRACTION82.3706
3.34-3.6590.232330.1714065X-RAY DIFFRACTION99.3987
3.659-4.0910.221760.1513738X-RAY DIFFRACTION99.6182
4.091-4.7230.1681730.1293289X-RAY DIFFRACTION99.7407
4.723-5.7830.2071620.1442806X-RAY DIFFRACTION99.7647
5.783-8.1720.2031190.1432231X-RAY DIFFRACTION99.6607
8.172-64.4420.241690.1671286X-RAY DIFFRACTION98.9051

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