[English] 日本語
Yorodumi
- PDB-5ua7: Ocellatin-LB2, solution structure in SDS micelle by NMR spectroscopy -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ua7
TitleOcellatin-LB2, solution structure in SDS micelle by NMR spectroscopy
ComponentsOcellatin-LB2
KeywordsANTIMICROBIAL PROTEIN / OCELLATIN / ANTIMICROBIAL PEPTIDE / ALPHA HELIX / AMPHIPATHIC CHARACTER / C-TERMINAL CARBOXYAMIDATION
Function / homologyOcellatin / Ocellatin family / hemolysis by symbiont of host erythrocytes / defense response to bacterium / extracellular region / Ocellatin-LB2
Function and homology information
Biological speciesLeptodactylus labyrinthicus (frog)
MethodSOLUTION NMR / simulated annealing
AuthorsGusmao, K.A.G. / dos Santos, D.M. / Santos, V.M. / Pilo-Veloso, D. / de Lima, M.E. / Resende, J.M.
CitationJournal: Peptides / Year: 2018
Title: NMR structures in different membrane environments of three ocellatin peptides isolated from Leptodactylus labyrinthicus.
Authors: Gomes, K.A.G.G. / Dos Santos, D.M. / Santos, V.M. / Pilo-Veloso, D. / Mundim, H.M. / Rodrigues, L.V. / Liao, L.M. / Verly, R.M. / de Lima, M.E. / Resende, J.M.
History
DepositionDec 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.2Apr 11, 2018Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_nmr_ensemble / pdbx_nmr_representative
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_ensemble.conformer_selection_criteria / _pdbx_nmr_ensemble.conformers_calculated_total_number
Revision 1.3Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ocellatin-LB2


Theoretical massNumber of molelcules
Total (without water)2,3101
Polymers2,3101
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide Ocellatin-LB2


Mass: 2309.751 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Leptodactylus labyrinthicus (frog) / References: UniProt: C0HKF2*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-1H TOCSY
131isotropic22D 1H-13C HSQC
141isotropic22D 1H-15N HMQC

-
Sample preparation

DetailsType: solution
Contents: 2 mM Ocellatin-LB2, 1 mM DSS, 400 mM d-25 SDS, 5 % 99.75 D2O, 95% H2O/5% D2O
Label: Ocellatin-LB2-SDS / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMOcellatin-LB2natural abundance1
1 mMDSSnatural abundance1
400 mMSDSd-251
5 %D2O99.751
Sample conditionsIonic strength: Null Not defined / Label: Ocellatin-LB2 / pH: 4 / Pressure: Ambient / Temperature: 303.15 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceIIIBrukerAvanceIII8001
Bruker AvanceIIIBrukerAvanceIII6002

-
Processing

NMR software
NameDeveloperClassification
xwinnmrBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloregeometry optimization
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
MolmolKoradi, Billeter and Wuthrichdata analysis
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntondata analysis
RefinementMethod: simulated annealing / Software ordinal: 7 / Details: X-PLOR NIH
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / 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