[English] 日本語
Yorodumi
- PDB-2kng: Solution structure of C-domain of Lsr2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kng
TitleSolution structure of C-domain of Lsr2
ComponentsProtein lsr2
KeywordsDNA BINDING PROTEIN / DNA-binding domain / Immune response
Function / homology
Function and homology information


DNA protection / cellular response to oxygen levels / nucleoid / response to iron ion / acyltransferase activity / peptidoglycan-based cell wall / response to hydrogen peroxide / regulation of DNA-templated transcription / DNA binding / plasma membrane ...DNA protection / cellular response to oxygen levels / nucleoid / response to iron ion / acyltransferase activity / peptidoglycan-based cell wall / response to hydrogen peroxide / regulation of DNA-templated transcription / DNA binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Lsr2 / Lsr2, dimerization domain / : / Lsr2 dimerization domain / Lsr2 DNA-binding domain / E3-binding domain / Dihydrolipoamide Transferase / E3-binding domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Nucleoid-associated protein Lsr2 / Nucleoid-associated protein Lsr2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsLi, Y. / Xia, B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Lsr2 is a nucleoid-associated protein that targets AT-rich sequences and virulence genes in Mycobacterium tuberculosis
Authors: Gordon, B.R. / Li, Y. / Wang, L. / Sintsova, A. / van Bakel, H. / Tian, S. / Navarre, W.W. / Xia, B. / Liu, J.
History
DepositionAug 22, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein lsr2


Theoretical massNumber of molelcules
Total (without water)6,1421
Polymers6,1421
Non-polymers00
Water00
1


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

-
Components

#1: Protein Protein lsr2


Mass: 6141.680 Da / Num. of mol.: 1 / Fragment: UNP residues 66-112
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: lsr2 / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / References: UniProt: P65648, UniProt: P9WIP7*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D CBCA(CO)NH
1413D HBHA(CO)NH
1513D (H)CCH-COSY
1613D 1H-15N NOESY
1713D 1H-13C NOESY

-
Sample preparation

DetailsContents: 0.8mM [U-13C; U-15N] Lsr2C-1, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.8 mM / Component: Lsr2C-1 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 100 / pH: 6 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
Amber9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer, Baxrefinement
Amber9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer, Baxprocessing
Amber9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer, Baxchemical shift assignment
Amber9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer, Baxdata analysis
Amber9Johnson, One Moon Scientificprocessing
Amber9Johnson, One Moon Scientificchemical shift assignment
Amber9Johnson, One Moon Scientificdata analysis
Amber9Duggan, Legge, Dyson, Wrightprocessing
Amber9Duggan, Legge, Dyson, Wrightchemical shift assignment
Amber9Duggan, Legge, Dyson, Wrightdata analysis
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, Kollmprocessing
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, Kollmchemical shift assignment
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, Kollmdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

+
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