[English] 日本語
Yorodumi
- PDB-2m8v: Solution Structure and Activity Study of Bovicin HJ50, a Particul... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2m8v
TitleSolution Structure and Activity Study of Bovicin HJ50, a Particular Type AII Lantibiotic
ComponentsBovA
KeywordsANTIBIOTIC / lantibiotic
Function / homologyLantibiotic, type A, Lactobacillales-type / Type-A lantibiotic / killing of cells of another organism / defense response to bacterium / signaling receptor binding / extracellular region / Lantibiotic
Function and homology information
Biological speciesStreptococcus equinus (bacteria)
MethodSOLUTION NMR / molecular dynamics, simulated annealing
Model detailslowest energy, model1
AuthorsZhang, J. / Feng, Y. / Wang, J. / Zhong, J.
CitationJournal: Biochem.J. / Year: 2014
Title: Type AII lantibiotic bovicin HJ50 with a rare disulfide bond: structure, structure-activity relationships and mode of action.
Authors: Zhang, J. / Feng, Y. / Teng, K. / Lin, Y. / Gao, Y. / Wang, J. / Zhong, J.
History
DepositionMay 29, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Data collection / Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_nmr_software / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 2.0Jul 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / struct_conn
Item: _database_2.pdbx_DOI / _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BovA


Theoretical massNumber of molelcules
Total (without water)3,4401
Polymers3,4401
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/peptide BovA / Bovicin HJ50


Mass: 3440.091 Da / Num. of mol.: 1 / Fragment: UNP residues 26-58
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus equinus (bacteria) / Strain: HJ50 / Gene: bovA / Production host: Escherichia coli (E. coli) / References: UniProt: Q83ZN8

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-13C HSQC
1212D DQF-COSY
1312D 1H-1H TOCSY
1412D 1H-1H NOESY
1522D 1H-13C HSQC
1622D 1H-1H TOCSY
1722D DQF-COSY
1822D 1H-1H NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM BovA-1, 50 mM [U-2H] sodium acetate-2, 0.01 % DSS-3, 90% H2O/10% D2O90% H2O/10% D2O
21 mM BovA-4, 50 mM [U-2H] sodium acetate-5, 0.01 % DSS-6, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMBovA-11
50 mMsodium acetate-2[U-2H]1
0.01 %DSS-31
1 mMBovA-42
50 mMsodium acetate-5[U-2H]2
0.01 %DSS-62
Sample conditionsIonic strength: 50 / pH: 5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospincollection
FelixAccelrys Software Inc.processing
NMRViewJJohnson, One Moon Scientificchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSrefinement
RefinementMethod: molecular dynamics, 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