[English] 日本語
Yorodumi
- PDB-1w9n: Isolation and characterization of epilancin 15X, a novel antibiot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1w9n
TitleIsolation and characterization of epilancin 15X, a novel antibiotic from a clinical strain of Staphylococcus epidermidis
ComponentsEPILANCIN 15X
KeywordsANTIBIOTIC / TYPE A LANTIBIOTIC / LANTHIONINE / ANTIBACTERIAL / THIOESTER
Function / homologyLantibiotic, type A, Pep5-type / Type A lantibiotic family / cytolysis / defense response to bacterium / signaling receptor binding / EPILANCIN 15X / Lantibiotic epilancin 15X
Function and homology information
Biological speciesSTAPHYLOCOCCUS EPIDERMIDIS (bacteria)
MethodSOLUTION NMR / ARIA
AuthorsEkkelenkamp, M. / Hanssen, M.G.M. / Hsu, S.-T.D. / de Jong, A. / Milatovic, D. / Verhoef, J. / van Nuland, N.A.J.
Citation
Journal: FEBS Lett. / Year: 2005
Title: Isolation and structural characterization of epilancin 15X, a novel lantibiotic from a clinical strain of Staphylococcus epidermidis.
Authors: Ekkelenkamp, M.B. / Hanssen, M. / Danny Hsu, S.T. / de Jong, A. / Milatovic, D. / Verhoef, J. / van Nuland, N.A.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2004
Title: The Nisin-Lipid II Complex Reveals a Pyrophosphate Cage that Provides a Blueprint for Novel Antibiotics
Authors: Hsu, S.-T.D. / Breukink, E. / Tischenko, E. / Lutters, M.A. / de Kruijff, B. / Kaptein, R. / Bonvin, A.M.J.J. / van Nuland, N.A.J.
#2: Journal: Biochemistry / Year: 2002
Title: Mapping the Targeted Membrane Pore Formation Mechanism by Solution NMR: The Nisin Z and Lipid II Interaction in Sds Micelles
Authors: Hsu, S.-T.D. / Breukink, E. / de Kruijff, B. / Kaptein, R. / Bonvin, A.M.J.J. / van Nuland, N.A.J.
#3: Journal: J.Biol.Chem. / Year: 2003
Title: NMR Study of Mersacidin and Lipid II Interaction in Dodecylphosphocholine Micelles. Conformational Changes are a Key to Antimicrobial Activity
Authors: Hsu, S.-T.D. / Breukink, E. / Bierbaum, G. / Sahl, H.-G. / De Kruijff, B. / Kaptein, R. / Bonvin, A.M.J.J. / Van Nuland, N.A.J.
History
DepositionOct 14, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary / Version format compliance
Revision 1.2Nov 30, 2012Group: Other
Revision 1.3May 2, 2018Group: Data collection / Database references
Category: citation / citation_author / pdbx_nmr_spectrometer
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _pdbx_nmr_spectrometer.model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 3.0May 1, 2024Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EPILANCIN 15X


Theoretical massNumber of molelcules
Total (without water)3,1891
Polymers3,1891
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LEAST TOTAL ENERGY
Representative

-
Components

#1: Protein/peptide EPILANCIN 15X


Type: Polypeptide / Class: Lantibiotic / Mass: 3188.962 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Epilancin 15X is a tricyclic peptide. thioether bonds with cysteine result in three rings along the peptide chain. Post Translational maturation of lantibiotics involves the enzymic ...Details: Epilancin 15X is a tricyclic peptide. thioether bonds with cysteine result in three rings along the peptide chain. Post Translational maturation of lantibiotics involves the enzymic conversion of Thr and Ser into dehydrated amino acids and the formation of thioether bonds with cysteine. This is followed by membrane translocation and cleavage of the modified precursor.
Source: (natural) STAPHYLOCOCCUS EPIDERMIDIS (bacteria) / Strain: 15X150 / References: UniProt: P86047, EPILANCIN 15X
Compound detailsEPILANCIN 15X IS A LINEAR TYPE A LANTIBIOTIC. THE LANTIBIOTICS ARE CHARACTERIZED BY LANTHIONINE ...EPILANCIN 15X IS A LINEAR TYPE A LANTIBIOTIC. THE LANTIBIOTICS ARE CHARACTERIZED BY LANTHIONINE AND/OR METHYLLANTHIONINE NONPROTEINOGENIC AMINO ACIDS. HERE, EPILANCIN 15X IS REPRESENTED BY THE SEQUENCE (SEQRES) GROUP: 1 NAME: EPILANCIN 15X CHAIN: A COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 31 DESCRIPTION: EPILANCIN 15X IS A TRICYCLIC PEPTIDE. THIOETHER BONDS WITH CYSTEINE RESULT IN THREE RINGS ALONG THE PEPTIDE CHAIN. CROSSLINK 12-16 LANTHIONINE (DAL-CYS) CROSSLINK 20-23 BETA-METHYLLANTHIONINE (DBB-CYS) CROSSLINK 22-25 BETA-METHYLLANTHIONINE (DBB-CYS)

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
1311H-13C HSQC
1411H-13C HMBC
251NOESY
261TOCSY
NMR detailsText: NONE

-
Sample preparation

DetailsContents: 10%WATER/90%D2O
Sample conditions
Conditions-IDPressure (kPa)Temperature (K)
11.0 atm283.0 K
21.0 atm283.0 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker DRXBrukerDRX7502

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1.1BRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
NMRViewstructure solution
RefinementMethod: ARIA / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST TOTAL 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://pdbjlvh1.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