[English] 日本語
Yorodumi
- PDB-5vo7: NMR Assignment and Structure of Thioredoxin (Rv1471 ortholog) fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vo7
TitleNMR Assignment and Structure of Thioredoxin (Rv1471 ortholog) from Mycobacterium smegmatis ATCC 700084 / mc(2)155
ComponentsThioredoxin
KeywordsELECTRON TRANSPORT / PROTEIN NMR Thioredoxin Mycobacterium smegmatis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / PROTEIN
Function / homology
Function and homology information


glycerol ether metabolic process / protein-disulfide reductase activity / cell redox homeostasis
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin / Thioredoxin
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBarnwal, R.P. / Varani, G. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Assignment and Structure of Thioredoxin (Rv1471 ortholog) type protein from Mycobacterium smegmatis ATCC 700084 / mc(2)155
Authors: Barnwal, R.P. / Varani, G.
History
DepositionMay 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1May 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)11,6341
Polymers11,6341
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1target function

-
Components

#1: Protein Thioredoxin


Mass: 11634.341 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Gene: trxA_2, ERS451418_06713 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D6J3B8, UniProt: O30974*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic22D 1H-13C HSQC
131isotropic23D CBCA(CO)NH
141isotropic23D HN(CA)CB
151isotropic23D HNCO
191isotropic23D (H)CCH-TOCSY
181isotropic23D HBHA(CO)NH
171isotropic13D 1H-15N NOESY
161isotropic13D 1H-13C NOESY

-
Sample preparation

DetailsType: solution
Contents: 1.1 mM [U-99% 13C; U-99% 15N] Thioredoxin (Rv1471 ortholog) from Mycobacterium smegmatis ATCC 700084 / mc(2)15513C, 93% H2O/7% D2O
Label: 13C 15N / Solvent system: 93% H2O/7% D2O
SampleConc.: 1.1 mM
Component: Thioredoxin (Rv1471 ortholog) from Mycobacterium smegmatis ATCC 700084 / mc(2)15513C
Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 100 mM / Label: Conditions_1 / pH: 6 / Pressure: AMBIENT atm / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8001
Bruker AVANCE IIBrukerAVANCE II6002

-
Processing

NMR software
NameVersionDeveloperClassification
CYANA3.97Guntert, Mumenthaler and Wuthrichrefinement
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
AnalysisCCPNchemical shift assignment
TopSpinBruker Biospincollection
CcpNMRCCPNpeak picking
CcpNMRCCPNdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / 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