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- PDB-8bqg: W-formate dehydrogenase from Desulfovibrio vulgaris - Soaking wit... -

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Basic information

Entry
Database: PDB / ID: 8bqg
TitleW-formate dehydrogenase from Desulfovibrio vulgaris - Soaking with Formate 1 min
Components(Formate dehydrogenase, ...) x 2
KeywordsOXIDOREDUCTASE / Formate / CO2 / Molybdenum and Tungsten enzymes / DMSO reductase family
Function / homology
Function and homology information


formate dehydrogenase (cytochrome-c-553) activity / formate dehydrogenase / formate dehydrogenase (NAD+) activity / molybdenum ion binding / molybdopterin cofactor binding / anaerobic respiration / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / 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 / Molydopterin 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
FORMIC ACID / 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 speciesDesulfovibrio vulgaris str. Hildenborough (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.946 Å
AuthorsVilela-Alves, G. / Mota, C. / Oliveira, A.R. / Manuel, R.R. / Pereira, I.C. / Romao, M.J.
Funding support Portugal, 5items
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
CitationJournal: Int J Mol Sci / Year: 2022
Title: Tracking W-Formate Dehydrogenase Structural Changes During Catalysis and Enzyme Reoxidation.
Authors: Vilela-Alves, G. / Manuel, R.R. / Oliveira, A.R. / Pereira, I.C. / Romao, M.J. / Mota, C.
History
DepositionNov 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)142,57717
Polymers138,9192
Non-polymers3,65815
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10380 Å2
ΔGint-137 kcal/mol
Surface area36920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.537, 122.778, 148.985
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.) Desulfovibrio vulgaris str. Hildenborough (bacteria)
Strain: Hildenborough / Gene: fdnG-1
Production host: Desulfovibrio vulgaris str. Hildenborough (bacteria)
Strain (production host): Hildenborough / References: UniProt: Q72EJ1
#2: Protein Formate dehydrogenase, beta subunit, putative


Mass: 26481.494 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris str. Hildenborough (bacteria)
Strain: Hildenborough / Gene: DVU_0588
Production host: Desulfovibrio vulgaris str. Hildenborough (bacteria)
Strain (production host): Hildenborough / References: UniProt: Q72EJ0

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Non-polymers , 9 types, 163 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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / 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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 44.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 24% 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: 0.8856 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Mar 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.946→94.93 Å / Num. obs: 73334 / % possible obs: 91.96 % / Redundancy: 4.33 % / CC1/2: 0.9971 / Net I/σ(I): 9.2
Reflection shellResolution: 1.95→2.07 Å / Num. unique obs: 3667 / CC1/2: 0.435

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata processing
STARANISOdata scaling
PHASERphasing
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SDR

6sdr


Resolution: 1.946→94.93 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.232 / WRfactor Rwork: 0.178 / SU B: 6.04 / SU ML: 0.159 / Average fsc free: 0.8701 / Average fsc work: 0.8885 / Cross valid method: FREE R-VALUE / ESU R: 0.222 / ESU R Free: 0.188
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2427 3564 4.861 %
Rwork0.1929 69752 -
all0.195 --
obs-73316 83.657 %
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: 38.302 Å2
Baniso -1Baniso -2Baniso -3
1-0.093 Å20 Å2-0 Å2
2---0.166 Å20 Å2
3---0.073 Å2
Refinement stepCycle: LAST / Resolution: 1.946→94.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9197 0 164 148 9509
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0139621
X-RAY DIFFRACTIONr_bond_other_d0.0020.0158893
X-RAY DIFFRACTIONr_angle_refined_deg1.6181.6513088
X-RAY DIFFRACTIONr_angle_other_deg1.2781.58420532
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.60151174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8722.293484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.847151554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1141557
X-RAY DIFFRACTIONr_chiral_restr0.0840.21224
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210858
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022214
X-RAY DIFFRACTIONr_nbd_refined0.2020.22041
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.28966
X-RAY DIFFRACTIONr_nbtor_refined0.1680.24657
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.24428
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2299
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0470.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1590.211
X-RAY DIFFRACTIONr_nbd_other0.220.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0340.21
X-RAY DIFFRACTIONr_mcbond_it3.2293.9114705
X-RAY DIFFRACTIONr_mcbond_other3.2293.914704
X-RAY DIFFRACTIONr_mcangle_it4.3925.865876
X-RAY DIFFRACTIONr_mcangle_other4.3925.865877
X-RAY DIFFRACTIONr_scbond_it3.5354.1534916
X-RAY DIFFRACTIONr_scbond_other3.5354.1544917
X-RAY DIFFRACTIONr_scangle_it5.1586.0987164
X-RAY DIFFRACTIONr_scangle_other5.1586.0977165
X-RAY DIFFRACTIONr_lrange_it6.55145.14310733
X-RAY DIFFRACTIONr_lrange_other6.55145.13810720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.946-1.9960.304230.326611X-RAY DIFFRACTION9.8954
1.996-2.0510.36800.3051626X-RAY DIFFRACTION27.3792
2.051-2.110.3451690.313862X-RAY DIFFRACTION66.343
2.11-2.1750.3242500.2875140X-RAY DIFFRACTION91.1859
2.175-2.2460.3312660.2785349X-RAY DIFFRACTION97.9588
2.246-2.3250.3312610.2645194X-RAY DIFFRACTION98.4835
2.325-2.4130.262630.2335027X-RAY DIFFRACTION98.4369
2.413-2.5110.2822740.2274790X-RAY DIFFRACTION98.3874
2.511-2.6230.2862280.2174681X-RAY DIFFRACTION98.9917
2.623-2.7510.3022360.214441X-RAY DIFFRACTION98.6501
2.751-2.90.2582180.2044255X-RAY DIFFRACTION98.6111
2.9-3.0760.2881970.2094031X-RAY DIFFRACTION98.2342
3.076-3.2880.2521690.1893781X-RAY DIFFRACTION98.3811
3.288-3.5510.221990.1773483X-RAY DIFFRACTION97.6658
3.551-3.890.2051550.1663206X-RAY DIFFRACTION96.5805
3.89-4.3490.1981670.1472872X-RAY DIFFRACTION95.3861
4.349-5.0210.1781350.1422533X-RAY DIFFRACTION95.1498
5.021-6.1480.241150.1652168X-RAY DIFFRACTION94.9667
6.148-8.6860.199880.1531729X-RAY DIFFRACTION95.4307
8.686-94.930.197710.158973X-RAY DIFFRACTION93.2976

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