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- PDB-8cm7: W-formate dehydrogenase M405A from Desulfovibrio vulgaris -

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Basic information

Entry
Database: PDB / ID: 8cm7
TitleW-formate dehydrogenase M405A from Desulfovibrio vulgaris
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 / 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: 2.117 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
Revision 1.3Oct 23, 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)140,38622
Polymers136,3662
Non-polymers4,01920
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11400 Å2
ΔGint-147 kcal/mol
Surface area37430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.874, 123.833, 149.891
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: 112376.906 Da / Num. of mol.: 1 / Mutation: M405A
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.: 1
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 , 9 types, 187 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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.31 Å3/Da / Density % sol: 46.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 30% 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: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.117→75.058 Å / Num. obs: 47566 / % possible obs: 92.3 % / Redundancy: 6.9 % / CC1/2: 0.994 / Net I/σ(I): 8.31
Reflection shellResolution: 2.117→2.298 Å / Num. unique obs: 2379 / CC1/2: 0.613

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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
Starting model: 6SDR

6sdr


Resolution: 2.117→75.058 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 7.881 / SU ML: 0.199 / Cross valid method: FREE R-VALUE / ESU R: 0.56 / ESU R Free: 0.283
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2518 2417 5.081 %
Rwork0.197 45148 -
all0.2 --
obs-47565 68.356 %
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: 38.585 Å2
Baniso -1Baniso -2Baniso -3
1--0.448 Å2-0 Å2-0 Å2
2--0.016 Å2-0 Å2
3---0.433 Å2
Refinement stepCycle: LAST / Resolution: 2.117→75.058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9149 0 185 167 9501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0139614
X-RAY DIFFRACTIONr_bond_other_d0.0010.0158905
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.65113070
X-RAY DIFFRACTIONr_angle_other_deg1.2161.58420550
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.58351170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.37122.206485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.223151552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9241558
X-RAY DIFFRACTIONr_chiral_restr0.0750.21219
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210830
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022216
X-RAY DIFFRACTIONr_nbd_refined0.2030.22062
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.28892
X-RAY DIFFRACTIONr_nbtor_refined0.1660.24570
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.24256
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2316
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0940.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1510.211
X-RAY DIFFRACTIONr_nbd_other0.2310.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.870.24
X-RAY DIFFRACTIONr_mcbond_it2.8173.984686
X-RAY DIFFRACTIONr_mcbond_other2.8173.984685
X-RAY DIFFRACTIONr_mcangle_it4.2395.9655854
X-RAY DIFFRACTIONr_mcangle_other4.2395.9655855
X-RAY DIFFRACTIONr_scbond_it2.9034.1814928
X-RAY DIFFRACTIONr_scbond_other2.9024.1814929
X-RAY DIFFRACTIONr_scangle_it4.476.1577168
X-RAY DIFFRACTIONr_scangle_other4.476.1577169
X-RAY DIFFRACTIONr_lrange_it6.41745.94310710
X-RAY DIFFRACTIONr_lrange_other6.40945.92910696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.117-2.1720.364160.276277X-RAY DIFFRACTION5.7564
2.172-2.2320.318280.266721X-RAY DIFFRACTION15.1191
2.232-2.2970.338700.2571242X-RAY DIFFRACTION27.3447
2.297-2.3670.328930.2671729X-RAY DIFFRACTION38.8818
2.367-2.4450.3021020.2712077X-RAY DIFFRACTION48.2934
2.445-2.5310.3421230.2652389X-RAY DIFFRACTION56.8069
2.531-2.6260.3611510.2652656X-RAY DIFFRACTION65.8611
2.626-2.7330.311770.2663175X-RAY DIFFRACTION82.1166
2.733-2.8550.3191960.2463680X-RAY DIFFRACTION98.3507
2.855-2.9940.3481950.2353558X-RAY DIFFRACTION99.9467
2.994-3.1560.2741700.2193429X-RAY DIFFRACTION99.9167
3.156-3.3470.2531800.2063221X-RAY DIFFRACTION99.9706
3.347-3.5780.2691740.1913024X-RAY DIFFRACTION99.5951
3.578-3.8650.2531620.182699X-RAY DIFFRACTION95.8459
3.865-4.2340.2011370.162633X-RAY DIFFRACTION100
4.234-4.7330.1841420.1482385X-RAY DIFFRACTION100
4.733-5.4640.2291020.1622131X-RAY DIFFRACTION100
5.464-6.690.248810.1851835X-RAY DIFFRACTION100
6.69-9.4510.199760.1641447X-RAY DIFFRACTION99.9344
9.451-75.0580.175420.216840X-RAY DIFFRACTION99.2126

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