[English] 日本語
Yorodumi
- PDB-2ka5: NMR Structure of the protein TM1081 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ka5
TitleNMR Structure of the protein TM1081
ComponentsPutative anti-sigma factor antagonist TM_1081
Keywordsstructural genomics / unknown function / TM1081 / Termotoga Marithima / Phosphoprotein / PSI-2 / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG
Function / homology
Function and homology information


anti-sigma factor antagonist activity
Similarity search - Function
Anti-sigma factor antagonist / STAS domain / Transcription Regulator spoIIAA / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative anti-sigma factor antagonist TM_1081
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsSerrano, P. / Geralt, M. / Mohanty, B. / Pedrini, B. / Horst, R. / Wuthrich, K. / Wilson, I. / Joint Center for Structural Genomics (JCSG)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Comparison of NMR and crystal structures highlights conformational isomerism in protein active sites.
Authors: Serrano, P. / Pedrini, B. / Geralt, M. / Jaudzems, K. / Mohanty, B. / Horst, R. / Herrmann, T. / Elsliger, M.A. / Wilson, I.A. / Wuthrich, K.
History
DepositionOct 30, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative anti-sigma factor antagonist TM_1081


Theoretical massNumber of molelcules
Total (without water)14,4501
Polymers14,4501
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 / 80structures with the least restraint violations
RepresentativeModel #1closest to the average

-
Components

#1: Protein Putative anti-sigma factor antagonist TM_1081


Mass: 14449.717 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Species: maritima / Gene: TM_1081 / Plasmid: MH4a / Species (production host): coli / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta / Variant (production host): DE3 / References: UniProt: Q9X0H0

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCA
1513D HN(CA)CB
1613D 1H-15N NOESY
1713D 1H-13C NOESY aromatic
1813D 1H-13C NOESY aliphatic
1913D H(CCO)NH

-
Sample preparation

DetailsContents: 1.3 mM [U-98% 13C; U-98% 15N] TM1081, 0.3 % sodium azide, 150 mM sodium chloride, 20 mM sodium phosphate, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.3 mMTM1081[U-98% 13C; U-98% 15N]1
0.3 %sodium azide1
150 mMsodium chloride1
20 mMsodium phosphate1
Sample conditionsIonic strength: 190 / pH: 6.5 / Pressure: ambient / Temperature: 313 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

-
Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CARAKeller and Wuthrichdata analysis
CARAKeller and Wuthrichchemical shift assignment
ASCANFiorito, F., Herrmann, T. Damberger, F. Fred, Wuthrich, K.chemical shift assignment
TopSpinBruker Biospindata analysis
TopSpinBruker Biospincollection
OPALLuginbuhl, Guntert, Billeter and Wuthrichrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 80 / 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