[English] 日本語
Yorodumi
- PDB-6wpb: NMR Structure of HSP1-NH2 antimicrobial peptide in presence of SD... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wpb
TitleNMR Structure of HSP1-NH2 antimicrobial peptide in presence of SDS-d25 micelles
ComponentsHSP1-NH2
KeywordsANTIMICROBIAL PROTEIN / antimicrobial peptide
Function / homologydefense response to fungus / killing of cells of another organism / defense response to bacterium / extracellular region / Hylaseptin-P1
Function and homology information
Biological speciesBoana punctata (polka-dot treefrog)
MethodSOLUTION NMR / simulated annealing
AuthorsVerly, R.M. / Gomes, I.P.
CitationJournal: Biochim Biophys Acta Biomembr / Year: 2020
Title: Membrane interactions of the anuran antimicrobial peptide HSP1-NH2: Different aspects of the association to anionic and zwitterionic biomimetic systems.
Authors: Gomes, I.P. / Santos, T.L. / de Souza, A.N. / Nunes, L.O. / Cardoso, G.A. / Matos, C.O. / Costa, L.M.F. / Liao, L.M. / Resende, J.M. / Verly, R.M.
History
DepositionApr 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HSP1-NH2


Theoretical massNumber of molelcules
Total (without water)1,3121
Polymers1,3121
Non-polymers00
Water00
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 #1closest to the average

-
Components

#1: Protein/peptide HSP1-NH2


Mass: 1311.594 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Boana punctata (polka-dot treefrog) / References: UniProt: P84292
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D NOESY
121isotropic12D TOCSY
131isotropic12D 1H-13C HSQC aliphatic

-
Sample preparation

DetailsType: micelle / Contents: 1 mM unlable HSP-1, 90% H2O/10% D2O / Details: 200 mM SDS-d25 micelles / Label: natural abundace / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: HSP-1 / Isotopic labeling: unlable
Sample conditionsDetails: 200 mM SDS-d25 micelles / Ionic strength: undifined Not defined / Label: SDS-d25 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker Bruker Avance III / Manufacturer: Bruker / Model: Bruker Avance III / Field strength: 500 MHz

-
Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
PROCHECK / PROCHECK-NMRLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntondata analysis
QUEENNabuurs, Spronk, Krieger, Maassen, Vriend and Vuisterdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
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://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