[English] 日本語
Yorodumi
- PDB-1l1k: NMR Identification and Characterization of the Flexible Regions i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1l1k
TitleNMR Identification and Characterization of the Flexible Regions in the 160 KD Molten Globule-like Aggregate of Barstar at Low pH
ComponentsBarstar
KeywordsPROTEIN BINDING / Barstar / low pH / 160 kD / aggregate
Function / homologyBarstar (barnase inhibitor) / Barstar (barnase inhibitor) / Barstar-like superfamily / cytoplasm / Barstar
Function and homology information
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsJuneja, J. / Bhavesh, N.S. / Udgaokar, J.B. / Hosur, R.V.
CitationJournal: Biochemistry / Year: 2002
Title: NMR identification and characterization of the flexible regions in the 160 kDa molten globule-like aggregate of barstar at low pH.
Authors: Juneja, J. / Bhavesh, N.S. / Udgaonkar, J.B. / Hosur, R.V.
History
DepositionFeb 18, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Barstar


Theoretical massNumber of molelcules
Total (without water)2,2551
Polymers2,2551
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)10 / 10target function
Representative

-
Components

#1: Protein/peptide Barstar / RIBONUCLEASE INHIBITOR


Mass: 2254.586 Da / Num. of mol.: 1 / Fragment: Flexible region (residues 1-20)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Gene: barstar / Plasmid: pMT316 / Production host: Escherichia coli (E. coli) / Strain (production host): MM294 / References: UniProt: P11540

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 15N-separated NOESY
131HNN, HN(C)N, 15N HSQC, HNCA, HN(CO)CA, CBCANH, CBCA(CO)NH, HNCO,
1412D TOCSY, 2D HSQC-TOCSY
161TOCSY
NMR detailsText: This structure was determined using standard 2D and 3D hetronuclear techniques.

-
Sample preparation

DetailsContents: 1.2 mM Barstar U-15N, 13C; / Solvent system: 90 % H2O, 10& D2O; pH 2.7
Sample conditionspH: 2.7 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
VNMR1Bvariancollection
Felix97MSIprocessing
DYANA1ETHstructure solution
DYANA1ETHrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 10 / Conformers submitted total number: 10

+
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