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- PDB-8cm5: W-formate dehydrogenase C872A from Desulfovibrio vulgaris -

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Basic information

Entry
Database: PDB / ID: 8cm5
TitleW-formate dehydrogenase C872A 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 / molybdopterin cofactor binding / cellular 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 ...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 speciesDesulfovibrio vulgaris str. Hildenborough (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsVilela-Alves, G. / Mota, C. / Klymanska, K. / Oliveira, A.R. / Manuel, R.R. / Pereira, I.C. / Romao, M.J.
Funding support Portugal, 9items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPTDC/BII-BBF/2050/2020 Portugal
Fundacao para a Ciencia e a TecnologiaSFRH/BD/116515/2016 Portugal
Fundacao para a Ciencia e a TecnologiaCOVID/BD/151766/2021 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 TecnologiaUIDB/04612/2020 Portugal
Fundacao para a Ciencia e a TecnologiaUIDP/04612/2020 Portugal
Fundacao para a Ciencia e a TecnologiaLA/P/0087/2020 Portugal
CitationJournal: Nat.Chem.Biol. / Year: 2024
Title: An allosteric redox switch involved in oxygen protection in a CO 2 reductase.
Authors: Oliveira, A.R. / Mota, C. / Vilela-Alves, G. / Manuel, R.R. / Pedrosa, N. / Fourmond, V. / Klymanska, K. / Leger, C. / Guigliarelli, B. / Romao, M.J. / Cardoso Pereira, I.A.
History
DepositionFeb 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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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
C: Formate dehydrogenase, alpha subunit, selenocysteine-containing
D: Formate dehydrogenase, beta subunit, putative
K: Formate dehydrogenase, alpha subunit, selenocysteine-containing
L: Formate dehydrogenase, beta subunit, putative
R: Formate dehydrogenase, alpha subunit, selenocysteine-containing
S: Formate dehydrogenase, beta subunit, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)558,72947
Polymers545,5788
Non-polymers13,15139
Water17,348963
1
A: Formate dehydrogenase, alpha subunit, selenocysteine-containing
B: Formate dehydrogenase, beta subunit, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,60611
Polymers136,3942
Non-polymers3,2129
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8860 Å2
ΔGint-142 kcal/mol
Surface area37600 Å2
MethodPISA
2
C: Formate dehydrogenase, alpha subunit, selenocysteine-containing
D: Formate dehydrogenase, beta subunit, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,71212
Polymers136,3942
Non-polymers3,31810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8740 Å2
ΔGint-141 kcal/mol
Surface area37700 Å2
MethodPISA
3
K: Formate dehydrogenase, alpha subunit, selenocysteine-containing
L: Formate dehydrogenase, beta subunit, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,71212
Polymers136,3942
Non-polymers3,31810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9140 Å2
ΔGint-138 kcal/mol
Surface area37520 Å2
MethodPISA
4
R: Formate dehydrogenase, alpha subunit, selenocysteine-containing
S: Formate dehydrogenase, beta subunit, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,69812
Polymers136,3942
Non-polymers3,30410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9100 Å2
ΔGint-143 kcal/mol
Surface area37420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.440, 261.055, 126.209
Angle α, β, γ (deg.)90.000, 90.576, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Formate dehydrogenase, ... , 2 types, 8 molecules ACKRBDLS

#1: Protein
Formate dehydrogenase, alpha subunit, selenocysteine-containing


Mass: 112404.961 Da / Num. of mol.: 4 / Mutation: C872A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris str. Hildenborough (bacteria)
Gene: fdnG-1
Production host: Desulfovibrio vulgaris str. Hildenborough (bacteria)
References: UniProt: Q72EJ1
#2: Protein
Formate dehydrogenase, beta subunit, putative


Mass: 23989.508 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris str. Hildenborough (bacteria)
Gene: DVU_0588
Production host: Desulfovibrio vulgaris str. Hildenborough (bacteria)
References: UniProt: Q72EJ0

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Non-polymers , 7 types, 1002 molecules

#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-W / TUNGSTEN ION


Mass: 183.840 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: W / Feature type: SUBJECT OF INVESTIGATION
#6: 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.: 8 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 963 / 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: 2.29 Å3/Da / Density % sol: 46.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350 (w/v), 0.1 M Tris-HCl pH 8.5 and 0.2 M CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.15→48.831 Å / Num. obs: 248226 / % possible obs: 96.8 % / Redundancy: 2.3 % / CC1/2: 0.998 / Net I/σ(I): 6.7
Reflection shellResolution: 2.15→2.19 Å / Num. unique obs: 12361 / CC1/2: 0.453

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→48.831 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.233 / WRfactor Rwork: 0.175 / SU B: 7.227 / SU ML: 0.178 / Average fsc free: 0.8801 / Average fsc work: 0.8963 / Cross valid method: FREE R-VALUE / ESU R: 0.281 / ESU R Free: 0.214
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2396 12240 4.932 %
Rwork0.184 235956 -
all0.187 --
obs-248196 96.766 %
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: 34.843 Å2
Baniso -1Baniso -2Baniso -3
1--0.199 Å2-0 Å2-1.52 Å2
2--0.418 Å2-0 Å2
3----0.189 Å2
Refinement stepCycle: LAST / Resolution: 2.15→48.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37154 0 560 963 38677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01338797
X-RAY DIFFRACTIONr_bond_other_d0.0010.01535794
X-RAY DIFFRACTIONr_angle_refined_deg1.671.6552811
X-RAY DIFFRACTIONr_angle_other_deg1.2551.58482652
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.81854742
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84722.3271960
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.213156276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.39115228
X-RAY DIFFRACTIONr_chiral_restr0.0870.24938
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0243892
X-RAY DIFFRACTIONr_gen_planes_other0.0010.028956
X-RAY DIFFRACTIONr_nbd_refined0.2060.27625
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.234421
X-RAY DIFFRACTIONr_nbtor_refined0.1670.218188
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.217120
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.21377
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.040.29
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1620.224
X-RAY DIFFRACTIONr_nbd_other0.1910.2131
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1820.222
X-RAY DIFFRACTIONr_mcbond_it3.1023.55618992
X-RAY DIFFRACTIONr_mcbond_other3.1023.55618991
X-RAY DIFFRACTIONr_mcangle_it4.5595.32623726
X-RAY DIFFRACTIONr_mcangle_other4.5595.32623727
X-RAY DIFFRACTIONr_scbond_it3.2153.81419805
X-RAY DIFFRACTIONr_scbond_other3.2173.81919758
X-RAY DIFFRACTIONr_scangle_it4.9115.59128893
X-RAY DIFFRACTIONr_scangle_other4.9145.59628846
X-RAY DIFFRACTIONr_lrange_it6.5640.36542545
X-RAY DIFFRACTIONr_lrange_other6.55740.36542438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.2060.3219270.29417519X-RAY DIFFRACTION97.7116
2.206-2.2660.3028860.26617205X-RAY DIFFRACTION97.9003
2.266-2.3320.3038290.2516748X-RAY DIFFRACTION97.9384
2.332-2.4040.2868500.23516201X-RAY DIFFRACTION97.6072
2.404-2.4820.2838540.22315539X-RAY DIFFRACTION97.0977
2.482-2.570.297810.21615044X-RAY DIFFRACTION96.5881
2.57-2.6670.2587300.20614683X-RAY DIFFRACTION97.6867
2.667-2.7750.2757940.19714054X-RAY DIFFRACTION97.755
2.775-2.8990.2556840.1913480X-RAY DIFFRACTION97.2535
2.899-3.040.2586440.18512948X-RAY DIFFRACTION97.4407
3.04-3.2050.2396440.1812175X-RAY DIFFRACTION96.7253
3.205-3.3990.2356120.17511459X-RAY DIFFRACTION96.2369
3.399-3.6330.2315810.1810837X-RAY DIFFRACTION96.8859
3.633-3.9240.2135110.15410044X-RAY DIFFRACTION96.0506
3.924-4.2980.1894860.1379165X-RAY DIFFRACTION95.4694
4.298-4.8050.1833900.1318192X-RAY DIFFRACTION94.039
4.805-5.5470.1964140.157349X-RAY DIFFRACTION96.1124
5.547-6.7910.2043010.1546196X-RAY DIFFRACTION95.0549
6.791-9.590.1732110.1414615X-RAY DIFFRACTION91.0566
9.59-48.8310.2621110.1922503X-RAY DIFFRACTION88.5201

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