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- PDB-8rcg: W-formate dehydrogenase M405S from Desulfovibrio vulgaris -

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Basic information

Entry
Database: PDB / ID: 8rcg
TitleW-formate dehydrogenase M405S from 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 / cellular respiration / molybdopterin cofactor binding / 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 / 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
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 speciesNitratidesulfovibrio vulgaris str. Hildenborough (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.005 Å
AuthorsVilela-Alves, G. / Manuel, R.R. / 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: Acta Crystallogr.,Sect.F / Year: 2024
Title: Structural and biochemical characterization of the M405S variant of Desulfovibrio vulgaris formate dehydrogenase.
Authors: Vilela-Alves, G. / Rebelo Manuel, R. / Pedrosa, N. / Cardoso Pereira, I.A. / Romao, M.J. / Mota, C.
History
DepositionDec 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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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)140,02516
Polymers136,3822
Non-polymers3,64214
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10170 Å2
ΔGint-135 kcal/mol
Surface area36950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.341, 127.226, 148.266
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: 112392.906 Da / Num. of mol.: 1 / Mutation: M405S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitratidesulfovibrio vulgaris str. Hildenborough (bacteria)
Strain: Hildenborough / Gene: fdnG-1
Production host: Nitratidesulfovibrio vulgaris str. Hildenborough (bacteria)
Strain (production host): Hildenborough / References: UniProt: Q72EJ1
#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: Nitratidesulfovibrio vulgaris str. Hildenborough (bacteria)
Strain (production host): Hildenborough / References: UniProt: Q72EJ0

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Non-polymers , 8 types, 258 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 / 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 / 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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.22 Å3/Da / Density % sol: 44.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 32% 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: ID30B / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.005→48.592 Å / Num. obs: 71441 / % possible obs: 93.02 % / Redundancy: 4.61 % / CC1/2: 0.996 / Net I/σ(I): 7.381
Reflection shellResolution: 2.005→2.118 Å / Num. unique obs: 3573 / CC1/2: 0.562

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
STARANISOdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.005→48.592 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 7.12 / SU ML: 0.179 / Cross valid method: FREE R-VALUE / ESU R: 0.26 / ESU R Free: 0.203
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2528 3497 4.899 %
Rwork0.2124 67878 -
all0.214 --
obs-71375 86.56 %
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: 40.166 Å2
Baniso -1Baniso -2Baniso -3
1-0.244 Å20 Å20 Å2
2---0.068 Å20 Å2
3----0.176 Å2
Refinement stepCycle: LAST / Resolution: 2.005→48.592 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9197 0 163 244 9604
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0139628
X-RAY DIFFRACTIONr_bond_other_d0.0010.0158893
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.65113103
X-RAY DIFFRACTIONr_angle_other_deg1.1421.58420536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.06951176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99822.309485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.611151554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0911557
X-RAY DIFFRACTIONr_chiral_restr0.0540.21225
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210882
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022214
X-RAY DIFFRACTIONr_nbd_refined0.1910.22073
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.29033
X-RAY DIFFRACTIONr_nbtor_refined0.160.24585
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.24274
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2392
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0480.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0560.25
X-RAY DIFFRACTIONr_nbd_other0.1830.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0390.23
X-RAY DIFFRACTIONr_mcbond_it1.9194.2184707
X-RAY DIFFRACTIONr_mcbond_other1.9194.2184706
X-RAY DIFFRACTIONr_mcangle_it3.0716.3235879
X-RAY DIFFRACTIONr_mcangle_other3.0716.3235880
X-RAY DIFFRACTIONr_scbond_it1.7394.3144921
X-RAY DIFFRACTIONr_scbond_other1.7364.3194885
X-RAY DIFFRACTIONr_scangle_it2.8476.4017175
X-RAY DIFFRACTIONr_scangle_other2.8496.4057139
X-RAY DIFFRACTIONr_lrange_it4.96148.26710826
X-RAY DIFFRACTIONr_lrange_other4.95248.26510800
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.005-2.0570.402210.333552X-RAY DIFFRACTION9.4993
2.057-2.1130.3381200.312529X-RAY DIFFRACTION45.414
2.113-2.1740.3392270.3124270X-RAY DIFFRACTION78.6189
2.174-2.2410.2882530.2964875X-RAY DIFFRACTION92.1971
2.241-2.3150.3382490.2884993X-RAY DIFFRACTION97.0741
2.315-2.3960.3052700.2774910X-RAY DIFFRACTION99.5197
2.396-2.4860.3332460.2724788X-RAY DIFFRACTION99.7622
2.486-2.5880.3122480.264595X-RAY DIFFRACTION99.8557
2.588-2.7030.3312260.2614429X-RAY DIFFRACTION99.8499
2.703-2.8350.3112030.2464252X-RAY DIFFRACTION99.8431
2.835-2.9880.2972080.2394021X-RAY DIFFRACTION99.717
2.988-3.1690.271810.2333865X-RAY DIFFRACTION99.5816
3.169-3.3880.2481910.2263589X-RAY DIFFRACTION99.1345
3.388-3.6590.2771620.2173317X-RAY DIFFRACTION98.8072
3.659-4.0080.2291590.1843051X-RAY DIFFRACTION97.7467
4.008-4.4810.1891630.1532720X-RAY DIFFRACTION97.0707
4.481-5.1730.2011250.1482455X-RAY DIFFRACTION97.1751
5.173-6.3340.1821050.1522094X-RAY DIFFRACTION96.9149
6.334-8.9490.164890.1281639X-RAY DIFFRACTION96.1603
8.949-48.5920.173510.154934X-RAY DIFFRACTION93.8095

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