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

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Basic information

Entry
Database: PDB / ID: 9rjw
TitleW-formate dehydrogenase from Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris) - aerobic soaked with 100 bar Kr
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 / KRYPTON / 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: 1.64 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)141,32631
Polymers136,4272
Non-polymers4,90029
Water10,683593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13030 Å2
ΔGint-135 kcal/mol
Surface area37060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.665, 128.313, 148.735
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: 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 , 9 types, 622 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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical
ChemComp-KR / KRYPTON


Mass: 83.798 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Kr / Feature type: SUBJECT OF INVESTIGATION
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 593 / 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: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 293 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: ID23-1 / Wavelength: 0.861 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.861 Å / Relative weight: 1
ReflectionResolution: 1.64→97.155 Å / Num. obs: 135242 / % possible obs: 96.49 % / Redundancy: 13.31 % / CC1/2: 0.9987 / Net I/σ(I): 14.08
Reflection shellResolution: 1.64→1.733 Å / Num. unique obs: 6762 / CC1/2: 0.6367

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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: 1.64→97.155 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.607 / SU ML: 0.084 / Cross valid method: FREE R-VALUE / ESU R: 0.109 / ESU R Free: 0.106
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2187 6672 4.933 %
Rwork0.1877 128570 -
all0.189 --
obs-135242 89.068 %
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: 29.348 Å2
Baniso -1Baniso -2Baniso -3
1-0.216 Å20 Å2-0 Å2
2---0.166 Å20 Å2
3----0.051 Å2
Refinement stepCycle: LAST / Resolution: 1.64→97.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9234 0 187 593 10014
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0139672
X-RAY DIFFRACTIONr_bond_other_d0.0010.0158936
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.6513155
X-RAY DIFFRACTIONr_angle_other_deg1.371.58420630
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.17751178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09722.284486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.044151557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6571557
X-RAY DIFFRACTIONr_chiral_restr0.0850.21228
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0210900
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022224
X-RAY DIFFRACTIONr_nbd_refined0.2130.22080
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.28972
X-RAY DIFFRACTIONr_nbtor_refined0.1690.24745
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.24398
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2555
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0630.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0570.27
X-RAY DIFFRACTIONr_nbd_other0.1890.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0850.24
X-RAY DIFFRACTIONr_mcbond_it2.4542.9484721
X-RAY DIFFRACTIONr_mcbond_other2.4542.9474720
X-RAY DIFFRACTIONr_mcangle_it3.2384.4175896
X-RAY DIFFRACTIONr_mcangle_other3.2384.4175897
X-RAY DIFFRACTIONr_scbond_it2.9423.1714951
X-RAY DIFFRACTIONr_scbond_other2.9413.1714952
X-RAY DIFFRACTIONr_scangle_it4.2674.6437211
X-RAY DIFFRACTIONr_scangle_other4.2674.6437212
X-RAY DIFFRACTIONr_lrange_it5.36234.90711157
X-RAY DIFFRACTIONr_lrange_other5.32534.75911062
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.6830.27300.276760X-RAY DIFFRACTION7.1306
1.683-1.7290.312460.2844925X-RAY DIFFRACTION47.5932
1.729-1.7790.294960.2819461X-RAY DIFFRACTION94.6393
1.779-1.8340.2865090.2519730X-RAY DIFFRACTION99.9512
1.834-1.8940.255060.2319449X-RAY DIFFRACTION99.99
1.894-1.960.2534920.2279154X-RAY DIFFRACTION100
1.96-2.0340.2684770.2258788X-RAY DIFFRACTION100
2.034-2.1170.2564280.2258519X-RAY DIFFRACTION100
2.117-2.2110.2684260.2188176X-RAY DIFFRACTION100
2.211-2.3190.2483990.2137851X-RAY DIFFRACTION100
2.319-2.4450.2393950.2057402X-RAY DIFFRACTION100
2.445-2.5930.2273730.1997073X-RAY DIFFRACTION100
2.593-2.7720.2583470.1916624X-RAY DIFFRACTION100
2.772-2.9940.2163140.1926233X-RAY DIFFRACTION100
2.994-3.280.1962620.1865767X-RAY DIFFRACTION100
3.28-3.6670.1992620.1795203X-RAY DIFFRACTION100
3.667-4.2330.1782460.1454619X-RAY DIFFRACTION100
4.233-5.1840.1622120.1323928X-RAY DIFFRACTION100
5.184-7.3260.1941630.1473098X-RAY DIFFRACTION99.9693
7.326-97.1550.159890.1461810X-RAY DIFFRACTION99.6327

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