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

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Basic information

Entry
Database: PDB / ID: 8bqh
TitleW-formate dehydrogenase from Desulfovibrio vulgaris - Soaking with Formate 1.5 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 / 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 / Alpha-Beta Plaits - #20 / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
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: 1.61 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 1.2Oct 16, 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)143,67732
Polymers138,9192
Non-polymers4,75830
Water10,034557
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13160 Å2
ΔGint-147 kcal/mol
Surface area36170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.361, 127.456, 128.952
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 , 11 types, 587 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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#10: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#11: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 557 / 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 Å3/Da / Density % sol: 38.59 %
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: 1.61→90.65 Å / Num. obs: 94816 / % possible obs: 94.14 % / Redundancy: 5.7 % / CC1/2: 0.996 / Net I/σ(I): 9.5
Reflection shellResolution: 1.61→1.78 Å / Num. unique obs: 4742 / CC1/2: 0.6555

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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: 1.61→90.65 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.111 / SU ML: 0.069 / Cross valid method: FREE R-VALUE / ESU R: 0.124 / ESU R Free: 0.108
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1754 4778 5.039 %
Rwork0.1509 90038 -
all0.152 --
obs-94816 68.517 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.364 Å2
Baniso -1Baniso -2Baniso -3
1-0.132 Å20 Å20 Å2
2---0.062 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.61→90.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9126 0 230 557 9913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0139615
X-RAY DIFFRACTIONr_bond_other_d0.0020.0158905
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.65113054
X-RAY DIFFRACTIONr_angle_other_deg1.4521.58420565
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.89451170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.37322.25480
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.409151542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1591557
X-RAY DIFFRACTIONr_chiral_restr0.0890.21219
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0210816
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022204
X-RAY DIFFRACTIONr_nbd_refined0.2110.21974
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.28878
X-RAY DIFFRACTIONr_nbtor_refined0.1730.24719
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.24317
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2540
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1420.214
X-RAY DIFFRACTIONr_nbd_other0.2130.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2860.29
X-RAY DIFFRACTIONr_mcbond_it2.9261.7724683
X-RAY DIFFRACTIONr_mcbond_other2.9271.7724684
X-RAY DIFFRACTIONr_mcangle_it3.9132.6495852
X-RAY DIFFRACTIONr_mcangle_other3.9132.6495853
X-RAY DIFFRACTIONr_scbond_it4.562.1334932
X-RAY DIFFRACTIONr_scbond_other4.5722.1384895
X-RAY DIFFRACTIONr_scangle_it6.183.0177154
X-RAY DIFFRACTIONr_scangle_other6.183.0177155
X-RAY DIFFRACTIONr_lrange_it7.28221.32110917
X-RAY DIFFRACTIONr_lrange_other7.26421.17410830
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.6490.189120.233214X-RAY DIFFRACTION2.2277
1.649-1.6940.309400.246833X-RAY DIFFRACTION8.828
1.694-1.7430.256920.2421707X-RAY DIFFRACTION18.7787
1.743-1.7970.231490.2252741X-RAY DIFFRACTION31.0019
1.797-1.8560.2442290.2184472X-RAY DIFFRACTION51.9792
1.856-1.9210.2163100.2045790X-RAY DIFFRACTION69.6188
1.921-1.9940.2113420.1876374X-RAY DIFFRACTION79.2355
1.994-2.0750.23760.1817085X-RAY DIFFRACTION91.3778
2.075-2.1670.1853860.177178X-RAY DIFFRACTION96.6892
2.167-2.2730.1794090.1576931X-RAY DIFFRACTION98.1808
2.273-2.3960.1793270.1466782X-RAY DIFFRACTION99.3016
2.396-2.5410.1663400.1366406X-RAY DIFFRACTION99.9111
2.541-2.7160.1593440.136043X-RAY DIFFRACTION99.8125
2.716-2.9340.1582700.1325659X-RAY DIFFRACTION99.6136
2.934-3.2140.1662620.1345197X-RAY DIFFRACTION99.4353
3.214-3.5930.1572500.1364647X-RAY DIFFRACTION98.1559
3.593-4.1480.162330.1284142X-RAY DIFFRACTION98.8924
4.148-5.0790.1371850.1263536X-RAY DIFFRACTION98.4652
5.079-7.1770.1771250.1662764X-RAY DIFFRACTION96.7515
7.177-90.650.211970.1681537X-RAY DIFFRACTION94.5602

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