[English] 日本語
Yorodumi
- PDB-2l6d: Solution structure of desulfothioredoxin from Desulfovibrio vulga... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2l6d
TitleSolution structure of desulfothioredoxin from Desulfovibrio vulgaris Hildenborough in its reduced form
ComponentsThioredoxin
KeywordsOXIDOREDUCTASE / thioredoxin fold
Function / homology
Function and homology information


Glutaredoxin / Glutaredoxin domain profile. / Thioredoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin, putative
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsGarcin, E.B. / Bornet, O. / Sebban-Kreuzer, C. / Guerlesquin, F.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural and mechanistic insights into unusual thiol disulfide oxidoreductase.
Authors: Garcin, E.B. / Bornet, O. / Elantak, L. / Vita, N. / Pieulle, L. / Guerlesquin, F. / Sebban-Kreuzer, C.
History
DepositionNov 18, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2011Group: Database references
Revision 1.2Feb 1, 2012Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)12,3841
Polymers12,3841
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein Thioredoxin /


Mass: 12384.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Strain: Hildenborough / ATCC 29579 / NCIMB 8303 / Gene: DVU_0378 / Plasmid: pJF / Production host: Escherichia coli (E. coli) / References: UniProt: Q72F37

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-1H TOCSY
1412D 1H-1H NOESY
1513D CBCA(CO)NH
1613D HNCO
1713D HNCA
1813D HN(CA)CB
1913D HBHA(CO)NH
11013D HN(CO)CA
11113D (H)CCH-TOCSY
11213D 1H-15N NOESY
11313D 1H-13C NOESY
11412D 1H-15N HSQC
11512D 1H-13C HSQC
11612D 1H-1H TOCSY
11712D 1H-1H NOESY
11813D CBCA(CO)NH
11913D HN(CA)CB
12013D HNCA
12113D HN(CO)CA
12213D HNCO
12313D HBHA(CO)NH
12413D (H)CCH-TOCSY
12513D 1H-15N NOESY
12613D 1H-13C NOESY

-
Sample preparation

DetailsContents: 1 mM [U-99% 13C; U-99% 15N] reduced desulfothioredoxin, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: reduced desulfothioredoxin / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 0.1 / pH: 5.5 / Pressure: ambient / Temperature: 290 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
AmberCase, D.A. et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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