[English] 日本語
Yorodumi
- PDB-6gs9: NMR structure of aurein 2.5 in SDS micelles -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6gs9
TitleNMR structure of aurein 2.5 in SDS micelles
ComponentsAurein 2.5
KeywordsANTIMICROBIAL PROTEIN / AMP / aurein 2.5 / SDS micelle
Function / homology
Function and homology information


defense response to fungus / killing of cells of another organism / defense response to bacterium / lipid binding / extracellular region / membrane
Similarity search - Function
Frog skin active peptide family / Frog antimicrobial peptide, propeptide / Frog skin active peptide family signal and propeptide
Similarity search - Domain/homology
Biological speciesLitoria aurea (green and golden bell frog)
MethodSOLUTION NMR / simulated annealing / distance geometry
AuthorsManzo, G. / Mason, J.A.
CitationJournal: Sci Rep / Year: 2019
Title: Temporin L and aurein 2.5 have identical conformations but subtly distinct membrane and antibacterial activities.
Authors: Manzo, G. / Ferguson, P.M. / Hind, C.K. / Clifford, M. / Gustilo, V.B. / Ali, H. / Bansal, S.S. / Bui, T.T. / Drake, A.F. / Atkinson, R.A. / Sutton, J.M. / Lorenz, C.D. / Phoenix, D.A. / Mason, A.J.
History
DepositionJun 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Aug 14, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_nmr_representative / pdbx_nmr_spectrometer
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_representative.conformer_id / _pdbx_nmr_spectrometer.model
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
Revision 1.4Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aurein 2.5


Theoretical massNumber of molelcules
Total (without water)1,6521
Polymers1,6521
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1730 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1none

-
Components

#1: Protein/peptide Aurein 2.5


Mass: 1651.987 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Litoria aurea (green and golden bell frog) / References: UniProt: P69019*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY

-
Sample preparation

DetailsType: micelle
Contents: 2 mM Aurein 2.5, 100 mM [U-98% 2H] deuterated sodium dodecyl sulphate, 0.05 % w/w 2H 3-(Trimethylsilyl)propionic-2,2,3,3-d4 acid sodium salt, 90% H2O/10% D2O
Details: 100 mM of SDS-d25 was used to solubilise 2mM of peptide to have a L/P ratio of 50
Label: Aurein25_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMAurein 2.5natural abundance1
100 mMdeuterated sodium dodecyl sulphate[U-98% 2H]1
0.05 % w/w3-(Trimethylsilyl)propionic-2,2,3,3-d4 acid sodium salt2H1
Sample conditionsIonic strength: no salts Not defined / Label: Aur25_conditions / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 700 MHz

-
Processing

NMR software
NameDeveloperClassification
DYNAMODelaglio and Kuszewskirefinement
DYNAMODelaglio and Kuszewskistructure calculation
CARAKeller and Wuthrichchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
TopSpinBruker Biospinprocessing
Refinement
MethodSoftware ordinal
simulated annealing2
distance geometry1
NMR representativeSelection criteria: none
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / 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