[English] 日本語
Yorodumi
- PDB-2kpp: Solution NMR structure of Lin0431 protein from Listeria innocua. ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kpp
TitleSolution NMR structure of Lin0431 protein from Listeria innocua. Northeast Structural Genomics Consortium Target LkR112
ComponentsLin0431 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / solution NMR structure / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyN-utilization substance G protein NusG, insert domain / NusG, domain 2 / NusG, domain 2 superfamily / NusG domain II / mini-chromosome maintenance (MCM) complex, domain 2 / Sandwich / Mainly Beta / Lin0431 protein
Function and homology information
Biological speciesListeria innocua (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsTang, Y. / Xiao, R. / Ciccosanti, C. / Janjua, H. / Lee, D.Y. / Everett, J.K. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proteins / Year: 2010
Title: Solution NMR structure of Lin0431 protein from Listeria innocua reveals high structural similarity with domain II of bacterial transcription antitermination protein NusG.
Authors: Tang, Y. / Xiao, R. / Ciccosanti, C. / Janjua, H. / Lee, D.Y. / Everett, J.K. / Swapna, G.V. / Acton, T.B. / Rost, B. / Montelione, G.T.
History
DepositionOct 18, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lin0431 protein


Theoretical massNumber of molelcules
Total (without water)12,8091
Polymers12,8091
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Lin0431 protein


Mass: 12808.544 Da / Num. of mol.: 1 / Fragment: sequence database residues 36-140
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua (bacteria) / Gene: lin0431 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92EM7

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1322D High Resolution 1H-13C HSQC
1412D aromatic 1H-13C HSQC
1513D HNCO
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D HN(COCA)CB
1913D (H)CCH-COSY
11013D (H)CCH-TOCSY
11113D CCH-TOCSY
11213D 1H-13C aliphatic NOESY
11313D 1H-13C aromatic NOESY
11413D simutaeous NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.851 mM [U-100% 13C; U-100% 15N] LkR112, 20 mM MES, 200 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % NaN3, 50 uM DSS, 95% H2O/5% D2O95% H2O/5% D2O
20.887 mM [U-5% 13C; U-100% 15N] LkR112, 20 mM MES, 200 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % NaN3, 50 uM DSS, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.851 mMLkR112-1[U-100% 13C; U-100% 15N]1
20 mMMES-21
200 mMNaCl-31
5 mMCaCl2-41
10 mMDTT-51
0.02 %NaN3-61
50 uMDSS-71
0.887 mMLkR112-8[U-5% 13C; U-100% 15N]2
20 mMMES-92
200 mMNaCl-102
5 mMCaCl2-112
10 mMDTT-122
0.02 %NaN3-132
50 uMDSS-142
Sample conditionsIonic strength: 200 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
Sparky3.11Goddarddata analysis
AutoStructure2.2.1Huang, Tejero, Powers and Montelionestructure solution
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
PSVSBhattacharya and Montelionestructure validation
PdbStat5.1Tejero and Montelionepdb 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

+
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