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

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Basic information

Entry
Database: PDB / ID: 9rjx
TitleW-formate dehydrogenase from Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris) - Soaking with Formamide
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
FORMAMIDE / HYDROSULFURIC ACID / Chem-MGD / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 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: 1.734 Å
AuthorsVilela-Alves, G. / Manuel, R.R. / 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)141,29836
Polymers136,4272
Non-polymers4,87134
Water6,539363
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14380 Å2
ΔGint-124 kcal/mol
Surface area36580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.094, 148.557, 64.212
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 , 10 types, 397 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-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#10: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#11: Chemical
ChemComp-ARF / FORMAMIDE


Type: L-peptide NH3 amino terminus / Mass: 45.041 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CH3NO / Feature type: SUBJECT OF INVESTIGATION
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.15 Å3/Da / Density % sol: 42.84 %
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: ID23-1 / Wavelength: 0.7749 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.734→94.784 Å / Num. obs: 86871 / % possible obs: 92.85 % / Redundancy: 4.48 % / CC1/2: 0.9966 / Net I/σ(I): 8.54
Reflection shellResolution: 1.734→1.887 Å / Num. unique obs: 4344 / CC1/2: 0.6057

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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: 1.734→94.784 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.936 / SU ML: 0.117 / Cross valid method: FREE R-VALUE / ESU R: 0.18 / ESU R Free: 0.155
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.228 4436 5.107 %
Rwork0.1916 82433 -
all0.193 --
obs-86869 70.898 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 29.479 Å2
Baniso -1Baniso -2Baniso -3
1--0.146 Å2-0 Å2-0 Å2
2--0.022 Å2-0 Å2
3---0.124 Å2
Refinement stepCycle: LAST / Resolution: 1.734→94.784 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9168 0 244 363 9775
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0139666
X-RAY DIFFRACTIONr_bond_other_d0.0010.0158969
X-RAY DIFFRACTIONr_angle_refined_deg1.271.65213115
X-RAY DIFFRACTIONr_angle_other_deg1.1511.58820687
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.98651175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.69122.277483
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.255151553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9581557
X-RAY DIFFRACTIONr_chiral_restr0.0570.21223
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210910
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022282
X-RAY DIFFRACTIONr_nbd_refined0.1850.21925
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.28740
X-RAY DIFFRACTIONr_nbtor_refined0.1580.24588
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.24151
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2427
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1460.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1720.213
X-RAY DIFFRACTIONr_nbd_other0.1930.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1250.29
X-RAY DIFFRACTIONr_mcbond_it2.5842.9564718
X-RAY DIFFRACTIONr_mcbond_other2.5842.9564718
X-RAY DIFFRACTIONr_mcangle_it3.6554.425874
X-RAY DIFFRACTIONr_mcangle_other3.6544.425875
X-RAY DIFFRACTIONr_scbond_it3.0183.1954948
X-RAY DIFFRACTIONr_scbond_other3.0173.1954949
X-RAY DIFFRACTIONr_scangle_it4.5574.6587190
X-RAY DIFFRACTIONr_scangle_other4.5574.6587191
X-RAY DIFFRACTIONr_lrange_it5.94833.98710716
X-RAY DIFFRACTIONr_lrange_other5.92833.9410673
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.734-1.7790.23150.311276X-RAY DIFFRACTION3.2402
1.779-1.8280.425600.3061191X-RAY DIFFRACTION14.3447
1.828-1.8810.3321150.2882356X-RAY DIFFRACTION29.0774
1.881-1.9390.3232020.2743399X-RAY DIFFRACTION43.7599
1.939-2.0020.2922360.2764742X-RAY DIFFRACTION61.7848
2.002-2.0720.282470.2655412X-RAY DIFFRACTION72.6537
2.072-2.1510.2963320.2585561X-RAY DIFFRACTION79.1644
2.151-2.2390.2662980.2425925X-RAY DIFFRACTION86.2867
2.239-2.3380.2723510.2266205X-RAY DIFFRACTION94.2496
2.338-2.4520.2763280.236203X-RAY DIFFRACTION98.314
2.452-2.5850.2683130.2155966X-RAY DIFFRACTION99.2413
2.585-2.7410.2543340.2025610X-RAY DIFFRACTION99.4645
2.741-2.9310.2493070.1935345X-RAY DIFFRACTION99.2449
2.931-3.1650.2152680.184938X-RAY DIFFRACTION99.2754
3.165-3.4670.2072540.1664535X-RAY DIFFRACTION98.6609
3.467-3.8760.1812050.1614150X-RAY DIFFRACTION98.4181
3.876-4.4750.1641870.1443668X-RAY DIFFRACTION98.0667
4.475-5.480.1881740.1533091X-RAY DIFFRACTION97.6668
5.48-7.7450.191400.172450X-RAY DIFFRACTION97.5518
7.745-94.7840.221700.1581411X-RAY DIFFRACTION95.7956

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