[English] 日本語
Yorodumi
- PDB-6b6v: Crystal structure of Desulfovibrio vulgaris carbon monoxide dehyd... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6b6v
TitleCrystal structure of Desulfovibrio vulgaris carbon monoxide dehydrogenase, as-isolated (protein batch 1), canonical C-cluster
ComponentsCarbon monoxide dehydrogenase
KeywordsOXIDOREDUCTASE / nickel-iron-sulfur (Ni-Fe-S) cluster / iron-sulfur (Fe-S) cluster / metalloenzyme
Function / homology
Function and homology information


anaerobic carbon monoxide dehydrogenase / anaerobic carbon-monoxide dehydrogenase activity / hydroxylamine reductase activity / nickel cation binding / generation of precursor metabolites and energy / peroxidase activity / response to hydrogen peroxide / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #30 / Rossmann fold - #2030 / Ni-containing CO dehydrogenase / CO dehydrogenase, alpha-bundle / Hydroxylamine reductase/Ni-containing CO dehydrogenase / Prismane/CO dehydrogenase family / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #30 / Rossmann fold - #2030 / Ni-containing CO dehydrogenase / CO dehydrogenase, alpha-bundle / Hydroxylamine reductase/Ni-containing CO dehydrogenase / Prismane/CO dehydrogenase family / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / IRON/SULFUR CLUSTER / FE(4)-NI(1)-S(4) CLUSTER / Carbon monoxide dehydrogenase
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWittenborn, E.C. / Drennan, C.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM069857 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM008334 United States
CitationJournal: Elife / Year: 2018
Title: Redox-dependent rearrangements of the NiFeS cluster of carbon monoxide dehydrogenase.
Authors: Wittenborn, E.C. / Merrouch, M. / Ueda, C. / Fradale, L. / Leger, C. / Fourmond, V. / Pandelia, M.E. / Dementin, S. / Drennan, C.L.
History
DepositionOct 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carbon monoxide dehydrogenase
B: Carbon monoxide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,77614
Polymers135,4322
Non-polymers2,34412
Water4,954275
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11180 Å2
ΔGint-147 kcal/mol
Surface area36340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.650, 111.960, 195.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Carbon monoxide dehydrogenase


Mass: 67715.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Gene: cooS, DVU_2098 / Production host: Desulfovibrio fructosivorans (bacteria)
References: UniProt: Q72A99, anaerobic carbon monoxide dehydrogenase

-
Non-polymers , 5 types, 287 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-XCC / FE(4)-NI(1)-S(4) CLUSTER / C CLUSTER


Mass: 410.333 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4NiS4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.0-1.1 M ammonium tartrate dibasic, pH 7, 6-9% v/v glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 2, 2014
RadiationMonochromator: Cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. obs: 50328 / % possible obs: 99.3 % / Redundancy: 4.2 % / Rsym value: 0.129 / Net I/σ(I): 9.8
Reflection shellResolution: 2.5→2.55 Å / Rsym value: 0.697

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JQK

1jqk


Resolution: 2.5→97.13 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.59
RfactorNum. reflection% reflection
Rfree0.2057 2185 4.34 %
Rwork0.161 --
obs0.163 50322 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→97.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9241 0 80 275 9596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049504
X-RAY DIFFRACTIONf_angle_d0.94512962
X-RAY DIFFRACTIONf_dihedral_angle_d20.7435772
X-RAY DIFFRACTIONf_chiral_restr0.0421498
X-RAY DIFFRACTIONf_plane_restr0.0041682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.55440.28571340.2322946X-RAY DIFFRACTION99
2.5544-2.61380.29651340.21472974X-RAY DIFFRACTION99
2.6138-2.67920.26981360.20712958X-RAY DIFFRACTION99
2.6792-2.75160.27291350.20722999X-RAY DIFFRACTION100
2.7516-2.83260.25761340.18592966X-RAY DIFFRACTION99
2.8326-2.9240.24451350.18632957X-RAY DIFFRACTION99
2.924-3.02850.22741340.17573003X-RAY DIFFRACTION99
3.0285-3.14980.22321390.17492960X-RAY DIFFRACTION99
3.1498-3.29310.25051320.17133012X-RAY DIFFRACTION100
3.2931-3.46680.21261390.15433009X-RAY DIFFRACTION100
3.4668-3.6840.20221350.14253009X-RAY DIFFRACTION99
3.684-3.96840.16911360.13732982X-RAY DIFFRACTION99
3.9684-4.36780.14731380.13053031X-RAY DIFFRACTION99
4.3678-4.99980.171400.12883062X-RAY DIFFRACTION100
4.9998-6.29910.19691380.16663059X-RAY DIFFRACTION99
6.2991-97.20340.18651460.1583210X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5768-0.05820.18520.58920.06130.80870.0175-0.1419-0.05840.1275-0.0256-0.03080.1388-0.0670.00980.2479-0.02280.0020.19340.00150.2733-0.9135-4.2092-4.1947
20.59320.04510.00370.5896-0.05240.64510.02110.06350.0393-0.1163-0.01990.0031-0.041-0.1520.00050.27360.01910.02240.2716-0.01670.2769-19.563313.9904-32.7522
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

+
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