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- PDB-8cm6: W-formate dehydrogenase C872A from Desulfovibrio vulgaris - with ... -

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Basic information

Entry
Database: PDB / ID: 8cm6
TitleW-formate dehydrogenase C872A from Desulfovibrio vulgaris - with Formamide
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 / 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 / : / 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
FORMAMIDE / 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: 1.416 Å
AuthorsVilela-Alves, G. / Mota, C. / 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 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: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,82452
Polymers272,7894
Non-polymers9,03548
Water30,9501718
1
A: Formate dehydrogenase, alpha subunit, selenocysteine-containing
B: Formate dehydrogenase, beta subunit, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,28629
Polymers136,3942
Non-polymers4,89127
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13190 Å2
ΔGint-149 kcal/mol
Surface area36830 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)140,53923
Polymers136,3942
Non-polymers4,14421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11620 Å2
ΔGint-145 kcal/mol
Surface area36480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.467, 74.949, 122.806
Angle α, β, γ (deg.)73.868, 89.135, 71.123
Int Tables number1
Space group name H-MP1

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Components

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Formate dehydrogenase, ... , 2 types, 4 molecules ACBD

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


Mass: 112404.961 Da / Num. of mol.: 2 / 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.: 2
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 , 11 types, 1766 molecules

#3: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-W / TUNGSTEN ION


Mass: 183.840 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: W / Feature type: SUBJECT OF INVESTIGATION
#5: 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.: 4 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#11: Chemical
ChemComp-ARF / FORMAMIDE


Type: L-peptide NH3 amino terminus / Mass: 45.041 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH3NO / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1718 / 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: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 34% 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: 0.7749 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.416→117.57 Å / Num. obs: 346803 / % possible obs: 92.3 % / Redundancy: 2 % / CC1/2: 0.997 / Net I/σ(I): 8.01
Reflection shellResolution: 1.416→1.54 Å / Num. unique obs: 17340 / CC1/2: 0.658

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata processing
STARANISO2.3.79 (20211010)data scaling
PHASERphasing
XDSdata reduction
Aimlessdata scaling
XSCALEdata scaling
pointlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.416→117.57 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.176 / WRfactor Rwork: 0.149 / SU B: 1.332 / SU ML: 0.049 / Average fsc free: 0.9325 / Average fsc work: 0.9386 / Cross valid method: FREE R-VALUE / ESU R: 0.068 / ESU R Free: 0.07
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1757 17188 4.956 %
Rwork0.1485 329615 -
all0.15 --
obs-346803 75.752 %
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: 18.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.066 Å2-0.058 Å20.01 Å2
2---0.059 Å2-0.016 Å2
3----0.039 Å2
Refinement stepCycle: LAST / Resolution: 1.416→117.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18544 0 438 1718 20700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01319587
X-RAY DIFFRACTIONr_bond_other_d0.0010.01518153
X-RAY DIFFRACTIONr_angle_refined_deg1.6961.6526624
X-RAY DIFFRACTIONr_angle_other_deg1.4751.58541931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.92752397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20322.33983
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.006153164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.68115115
X-RAY DIFFRACTIONr_chiral_restr0.0970.22483
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0222085
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024539
X-RAY DIFFRACTIONr_nbd_refined0.2130.23921
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.218036
X-RAY DIFFRACTIONr_nbtor_refined0.1740.29613
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.28901
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.21316
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1090.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2190.25
X-RAY DIFFRACTIONr_nbd_other0.1670.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.160.230
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0930.21
X-RAY DIFFRACTIONr_mcbond_it1.3981.729533
X-RAY DIFFRACTIONr_mcbond_other1.3981.729533
X-RAY DIFFRACTIONr_mcangle_it1.9772.57511910
X-RAY DIFFRACTIONr_mcangle_other1.9772.57611911
X-RAY DIFFRACTIONr_scbond_it2.4031.95210054
X-RAY DIFFRACTIONr_scbond_other2.4031.95210055
X-RAY DIFFRACTIONr_scangle_it3.6082.82114606
X-RAY DIFFRACTIONr_scangle_other3.6082.82114607
X-RAY DIFFRACTIONr_lrange_it4.46120.67422494
X-RAY DIFFRACTIONr_lrange_other4.46120.67422494
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.416-1.4530.303890.26317800.265338570.7660.8055.52030.257
1.453-1.4930.2622220.2542490.25329920.8290.83813.55180.242
1.493-1.5360.264840.24494200.245321220.8460.84630.83250.233
1.536-1.5840.2478860.232167210.233311960.8660.86656.43990.216
1.584-1.6350.2512090.225228640.226302000.8660.87779.71190.205
1.635-1.6930.22913620.209263900.21292430.8940.994.90130.187
1.693-1.7570.21412980.191259750.192281620.9120.91996.84330.168
1.757-1.8280.19912900.169250640.171271510.9320.93897.06460.148
1.828-1.910.17911920.153239170.155260250.9480.95496.48030.135
1.91-2.0030.18111560.143229960.145248240.9510.9697.29290.129
2.003-2.1110.17911730.137218990.139237050.9550.96597.32970.126
2.111-2.2390.16911360.132206890.134223530.9620.9797.63790.125
2.239-2.3940.14410500.125195130.126210160.9710.97497.84450.121
2.394-2.5850.1699410.128182180.13196090.9630.97297.70510.128
2.585-2.8320.1578870.131165140.133179710.9680.97296.82820.135
2.832-3.1660.1768600.145150910.147162370.9580.96798.23860.153
3.166-3.6560.1737040.149134200.15143590.9650.96998.36340.164
3.656-4.4760.1435730.122113890.123121430.9770.9898.50940.146
4.476-6.3250.164340.14387010.14493570.9760.97997.62740.174
6.325-117.570.1582420.14248080.14351500.9720.97298.05830.217

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