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- PDB-9rk1: W-formate dehydrogenase W491E from Nitratidesulfovibrio vulgaris ... -

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Basic information

Entry
Database: PDB / ID: 9rk1
TitleW-formate dehydrogenase W491E from Nitratidesulfovibrio vulgaris (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 / 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: 1.993 Å
AuthorsVilela-Alves, G. / Manuel, R.R. / Martins, G. / 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: 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)139,68415
Polymers136,2382
Non-polymers3,44613
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9870 Å2
ΔGint-134 kcal/mol
Surface area38290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.824, 128.043, 148.748
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: 112379.930 Da / Num. of mol.: 1 / Mutation: W491E
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 , 7 types, 212 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.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.04 Å3/Da / Density % sol: 39.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 30% 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: May 12, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.993→74.374 Å / Num. obs: 69547 / % possible obs: 93.2 % / Redundancy: 6.98 % / CC1/2: 0.9874 / Net I/σ(I): 7.12
Reflection shellResolution: 1.993→2.146 Å / Num. unique obs: 3477 / CC1/2: 0.5072

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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: 1.993→74.374 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.885 / SU B: 6.644 / SU ML: 0.175 / Cross valid method: FREE R-VALUE / ESU R: 0.266 / ESU R Free: 0.214
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2582 3530 5.076 %
Rwork0.2086 66017 -
all0.211 --
obs-69547 81.553 %
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: 35.311 Å2
Baniso -1Baniso -2Baniso -3
1-0.137 Å20 Å2-0 Å2
2---0.09 Å20 Å2
3----0.047 Å2
Refinement stepCycle: LAST / Resolution: 1.993→74.374 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9230 0 150 199 9579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0139650
X-RAY DIFFRACTIONr_bond_other_d0.0010.0158913
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.65113132
X-RAY DIFFRACTIONr_angle_other_deg1.0681.58420583
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.52151179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.64122.32487
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.914151561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6581557
X-RAY DIFFRACTIONr_chiral_restr0.0450.21229
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210898
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022218
X-RAY DIFFRACTIONr_nbd_refined0.1720.21807
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1680.28570
X-RAY DIFFRACTIONr_nbtor_refined0.1530.24550
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.24115
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2311
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1590.23
X-RAY DIFFRACTIONr_nbd_other0.1770.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1050.23
X-RAY DIFFRACTIONr_mcbond_it4.0323.6324722
X-RAY DIFFRACTIONr_mcbond_other4.0313.6324721
X-RAY DIFFRACTIONr_mcangle_it5.6785.445896
X-RAY DIFFRACTIONr_mcangle_other5.6785.445897
X-RAY DIFFRACTIONr_scbond_it3.9643.8234928
X-RAY DIFFRACTIONr_scbond_other3.9633.8234929
X-RAY DIFFRACTIONr_scangle_it5.695.6217187
X-RAY DIFFRACTIONr_scangle_other5.6895.6227188
X-RAY DIFFRACTIONr_lrange_it7.48441.25910493
X-RAY DIFFRACTIONr_lrange_other7.48441.26210477
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.993-2.0450.41850.271139X-RAY DIFFRACTION2.3125
2.045-2.1010.289650.3011095X-RAY DIFFRACTION19.0978
2.101-2.1620.3221580.3063036X-RAY DIFFRACTION53.9345
2.162-2.2280.3342530.2944390X-RAY DIFFRACTION80.9731
2.228-2.3010.3192470.2794773X-RAY DIFFRACTION90.304
2.301-2.3820.3052540.2724929X-RAY DIFFRACTION96.0526
2.382-2.4720.3032640.2614904X-RAY DIFFRACTION99.0798
2.472-2.5730.2792420.2514747X-RAY DIFFRACTION99.7002
2.573-2.6870.3222240.2534608X-RAY DIFFRACTION100
2.687-2.8190.3052470.2374380X-RAY DIFFRACTION100
2.819-2.9710.2672130.2284181X-RAY DIFFRACTION100
2.971-3.1510.2742060.2243953X-RAY DIFFRACTION100
3.151-3.3690.2791820.2213692X-RAY DIFFRACTION98.2003
3.369-3.6380.2412090.2043455X-RAY DIFFRACTION99.9182
3.638-3.9850.2461820.1793208X-RAY DIFFRACTION100
3.985-4.4550.2081540.1482932X-RAY DIFFRACTION100
4.455-5.1440.1961520.1422583X-RAY DIFFRACTION100
5.144-6.2980.2091160.1552227X-RAY DIFFRACTION100
6.298-8.8990.187900.1521759X-RAY DIFFRACTION100
8.899-74.3740.25670.1771026X-RAY DIFFRACTION99.8174

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