[English] 日本語
Yorodumi
- PDB-8cm4: W-formate dehydrogenase C872A from Desulfovibrio vulgaris - expos... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8cm4
TitleW-formate dehydrogenase C872A from Desulfovibrio vulgaris - exposed to oxygen
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
HYDROSULFURIC ACID / Chem-MGD / NITRATE ION / 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: 2.3 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 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)279,53726
Polymers272,7894
Non-polymers6,74822
Water6,413356
1
A: Formate dehydrogenase, alpha subunit, selenocysteine-containing
B: Formate dehydrogenase, beta subunit, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,83814
Polymers136,3942
Non-polymers3,44412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Formate dehydrogenase, alpha subunit, selenocysteine-containing
D: 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
Unit cell
Length a, b, c (Å)73.299, 126.897, 260.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
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)
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: 23989.508 Da / Num. of mol.: 2
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

-
Non-polymers , 8 types, 378 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.: 4 / 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.: 8 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-W / TUNGSTEN ION


Mass: 183.840 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: W / Feature type: SUBJECT OF INVESTIGATION
#7: 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
#8: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 22% PEG 3350 (w/v), 0.1 M Tris-HCl pH 8.5 and 0.2 M CaCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979181 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979181 Å / Relative weight: 1
ReflectionResolution: 2.3→148.12 Å / Num. obs: 108727 / % possible obs: 99.5 % / Redundancy: 4.5 % / CC1/2: 0.99 / Net I/σ(I): 8.4
Reflection shellResolution: 2.3→2.37 Å / Num. unique obs: 4478 / CC1/2: 0.698

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6sdr

6sdr


Resolution: 2.3→48.312 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.226 / WRfactor Rwork: 0.173 / SU B: 10.757 / SU ML: 0.242 / Average fsc free: 0.8432 / Average fsc work: 0.8652 / Cross valid method: FREE R-VALUE / ESU R: 0.399 / ESU R Free: 0.258
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2561 5427 4.991 %
Rwork0.2004 103300 -
all0.203 --
obs-108727 99.779 %
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: 42.628 Å2
Baniso -1Baniso -2Baniso -3
1--2.308 Å2-0 Å20 Å2
2--3.506 Å2-0 Å2
3----1.198 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.312 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18540 0 291 356 19187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01319366
X-RAY DIFFRACTIONr_bond_other_d0.0010.01517873
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.6526358
X-RAY DIFFRACTIONr_angle_other_deg1.1521.58441269
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.30952367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17422.331978
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.125153135
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.15415114
X-RAY DIFFRACTIONr_chiral_restr0.0720.22465
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0221905
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024467
X-RAY DIFFRACTIONr_nbd_refined0.1920.23866
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.217693
X-RAY DIFFRACTIONr_nbtor_refined0.1620.29123
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.28701
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2582
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0790.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1260.27
X-RAY DIFFRACTIONr_nbd_other0.1810.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1090.23
X-RAY DIFFRACTIONr_mcbond_it2.3694.4159480
X-RAY DIFFRACTIONr_mcbond_other2.3674.4159479
X-RAY DIFFRACTIONr_mcangle_it3.6776.61911843
X-RAY DIFFRACTIONr_mcangle_other3.6776.61911844
X-RAY DIFFRACTIONr_scbond_it2.4464.6349886
X-RAY DIFFRACTIONr_scbond_other2.4464.6349887
X-RAY DIFFRACTIONr_scangle_it4.0016.83514419
X-RAY DIFFRACTIONr_scangle_other4.0016.83414420
X-RAY DIFFRACTIONr_lrange_it5.70150.25721246
X-RAY DIFFRACTIONr_lrange_other5.69850.25321212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.3353930.3057585X-RAY DIFFRACTION99.8998
2.36-2.4240.3413590.3097336X-RAY DIFFRACTION99.6891
2.424-2.4950.3164110.2917115X-RAY DIFFRACTION99.7879
2.495-2.5710.333790.2726936X-RAY DIFFRACTION99.7818
2.571-2.6560.3153440.2586797X-RAY DIFFRACTION99.8322
2.656-2.7490.3123510.2486531X-RAY DIFFRACTION99.8839
2.749-2.8530.3122820.2316374X-RAY DIFFRACTION99.9099
2.853-2.9690.3033530.2246051X-RAY DIFFRACTION99.9064
2.969-3.1010.313260.2255843X-RAY DIFFRACTION99.9514
3.101-3.2520.2763060.2135621X-RAY DIFFRACTION99.9663
3.252-3.4280.2562760.2055313X-RAY DIFFRACTION99.5902
3.428-3.6360.2622590.1945066X-RAY DIFFRACTION99.9249
3.636-3.8870.2342430.1784774X-RAY DIFFRACTION99.8806
3.887-4.1980.2162050.1594458X-RAY DIFFRACTION99.6794
4.198-4.5980.1722140.1394125X-RAY DIFFRACTION99.7013
4.598-5.140.2072000.1473701X-RAY DIFFRACTION99.7443
5.14-5.9330.2381670.1723322X-RAY DIFFRACTION99.5719
5.933-7.2630.2351760.1852820X-RAY DIFFRACTION99.5018
7.263-10.2560.1931260.1482213X-RAY DIFFRACTION99.5319
10.256-48.3120.261570.2121319X-RAY DIFFRACTION98.0057

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more