[English] 日本語
Yorodumi
- PDB-2jr3: Antibacterial Peptide from Eggshell Matrix: Structure and Self-as... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jr3
TitleAntibacterial Peptide from Eggshell Matrix: Structure and Self-assembly of beta-defensin Like Peptide from the Chinese Soft-shelled Turtle Eggshell
ComponentsPelovaterin
KeywordsANTIMICROBIAL PROTEIN / beta-defensin Like Peptide / Chinese Soft-shelled Turtle Eggshell / Antibacterial Peptide / Eggshell Matrix
Function / homology
Function and homology information


biomineral tissue development / defense response to bacterium / extracellular region
Similarity search - Function
Anthopleurin-A - #60 / Pelovaterin / Pelovaterin / Anthopleurin-A / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Biological speciesPelodiscus sinensis (Chinese soft-shelled turtle)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsVivekanandan, S. / Lakshminarayanan, R. / Jois, S.D.S. / Perumal Samy, R. / Banerjee, Y. / Chi-Jin, E.O. / Teo, K.W. / Kini, R.M. / Valiyaveettil, S.
CitationJournal: J.Am.Chem.Soc. / Year: 2008
Title: Structure, self-assembly, and dual role of a beta-defensin-like peptide from the Chinese soft-shelled turtle eggshell matrix.
Authors: Lakshminarayanan, R. / Vivekanandan, S. / Samy, R.P. / Banerjee, Y. / Chi-Jin, E.O. / Teo, K.W. / Jois, S.D. / Kini, R.M. / Valiyaveettil, S.
History
DepositionJun 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _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 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pelovaterin


Theoretical massNumber of molelcules
Total (without water)4,1991
Polymers4,1991
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide Pelovaterin


Mass: 4198.853 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pelodiscus sinensis (Chinese soft-shelled turtle)
References: UniProt: P84818

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1312D DQF-COSY

-
Sample preparation

DetailsContents: 1 mM Pelovaterin, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: Pelovaterin
Sample conditionspH: 4.5 / Pressure: AMBIENT / Temperature: 308 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE5002

-
Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1P.GUNTERT ET AL.structure solution
CYANA2.1P.GUNTERT ET AL.refinement
Sparky3.11Goddarddata analysis
Sparky3.11Goddardpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage constraints per residue: 15
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum distance constraint violation: 3 Å / Maximum lower distance constraint violation: 0.19 Å / Maximum upper distance constraint violation: 0.31 Å

+
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