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

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Basic information

Entry
Database: PDB / ID: 8bqj
TitleW-formate dehydrogenase from Desulfovibrio vulgaris - Soaking with Formate 5 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 / cell envelope / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / metal ion binding
Similarity search - Function
Formate dehydrogenase-N, alpha subunit / : / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / 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 ...Formate dehydrogenase-N, alpha subunit / : / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
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: 2.107 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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)142,43915
Polymers138,9192
Non-polymers3,52013
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9940 Å2
ΔGint-135 kcal/mol
Surface area36940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.351, 150.550, 64.941
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 , 8 types, 92 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.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.28 Å3/Da / Density % sol: 46.14 %
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: 2.107→95.597 Å / Num. obs: 45854 / % possible obs: 92.88 % / Redundancy: 4.33 % / CC1/2: 0.9941 / Net I/σ(I): 9.051
Reflection shellResolution: 2.107→2.359 Å / Num. unique obs: 2293 / CC1/2: 0.552

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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: 2.107→95.597 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.92 / SU B: 8.155 / SU ML: 0.201 / Cross valid method: FREE R-VALUE / ESU R: 0.674 / ESU R Free: 0.282
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2449 2296 5.009 %
Rwork0.2139 43543 -
all0.215 --
obs-45839 64.818 %
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: 38.776 Å2
Baniso -1Baniso -2Baniso -3
1--0.555 Å2-0 Å2-0 Å2
2---0.261 Å20 Å2
3---0.816 Å2
Refinement stepCycle: LAST / Resolution: 2.107→95.597 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9197 0 155 79 9431
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0139614
X-RAY DIFFRACTIONr_bond_other_d0.0010.0158886
X-RAY DIFFRACTIONr_angle_refined_deg1.2341.6513082
X-RAY DIFFRACTIONr_angle_other_deg1.0781.58420516
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.84851174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.71122.293484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.623151554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9791557
X-RAY DIFFRACTIONr_chiral_restr0.0450.21224
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210855
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022213
X-RAY DIFFRACTIONr_nbd_refined0.180.21980
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1710.28998
X-RAY DIFFRACTIONr_nbtor_refined0.1560.24566
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.24277
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0190.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1180.29
X-RAY DIFFRACTIONr_nbd_other0.1490.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0010.21
X-RAY DIFFRACTIONr_mcbond_it1.6544.0794705
X-RAY DIFFRACTIONr_mcbond_other1.6544.0784704
X-RAY DIFFRACTIONr_mcangle_it2.7186.1185876
X-RAY DIFFRACTIONr_mcangle_other2.7186.1195877
X-RAY DIFFRACTIONr_scbond_it1.5154.1764909
X-RAY DIFFRACTIONr_scbond_other1.5154.1764910
X-RAY DIFFRACTIONr_scangle_it2.536.27158
X-RAY DIFFRACTIONr_scangle_other2.536.27159
X-RAY DIFFRACTIONr_lrange_it4.23546.71910603
X-RAY DIFFRACTIONr_lrange_other4.23546.7210599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.107-2.1610.41490.309250X-RAY DIFFRACTION4.9856
2.161-2.2210.325200.305335X-RAY DIFFRACTION7.1071
2.221-2.2850.354180.318432X-RAY DIFFRACTION9.1799
2.285-2.3550.313650.3061095X-RAY DIFFRACTION24.3595
2.355-2.4330.313980.2921601X-RAY DIFFRACTION36.7908
2.433-2.5180.341160.3072267X-RAY DIFFRACTION53.192
2.518-2.6130.3211600.2832849X-RAY DIFFRACTION69.685
2.613-2.720.3311860.2853445X-RAY DIFFRACTION87.1579
2.72-2.8410.3031780.2733755X-RAY DIFFRACTION98.3988
2.841-2.9790.3161770.2673629X-RAY DIFFRACTION99.5814
2.979-3.140.2981760.2443447X-RAY DIFFRACTION99.4237
3.14-3.3310.2871620.2233261X-RAY DIFFRACTION99.1312
3.331-3.560.2621590.2183077X-RAY DIFFRACTION98.9602
3.56-3.8460.2351440.2052863X-RAY DIFFRACTION98.4288
3.846-4.2120.2091440.1782610X-RAY DIFFRACTION98.3923
4.212-4.7090.1931340.1632387X-RAY DIFFRACTION98.0934
4.709-5.4370.1771200.1722147X-RAY DIFFRACTION98.9956
5.437-6.6560.2321070.1921808X-RAY DIFFRACTION99.0176
6.656-9.4040.182840.161435X-RAY DIFFRACTION98.5724
9.404-95.5970.153390.181850X-RAY DIFFRACTION97.7998

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