[English] 日本語
Yorodumi
- PDB-2ndn: NMR solution structure of PawS Derived Peptide 20 (PDP-20) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ndn
TitleNMR solution structure of PawS Derived Peptide 20 (PDP-20)
ComponentsPawS1a Derived Peptide 20
KeywordsPLANT PROTEIN / PDP / PawS Derived Peptide / plant peptide / cyclic peptide
Function / homologyProtease inhibitor/seed storage/LTP family / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / PawS1a
Function and homology information
Biological speciesZinnia haageana (plant)
MethodSOLUTION NMR / simulated annealing
Model detailsstructure with the best MOLPROBITY score, model1
AuthorsFranke, B. / Jayasena, A.S. / Fisher, M.F. / Swedberg, J.E. / Taylor, N.L. / Mylne, J.S. / Rosengren, K.
CitationJournal: Biopolymers / Year: 2016
Title: Diverse cyclic seed peptides in the Mexican zinnia (Zinnia haageana).
Authors: Franke, B. / Jayasena, A.S. / Fisher, M.F. / Swedberg, J.E. / Taylor, N.L. / Mylne, J.S. / Rosengren, K.J.
History
DepositionJul 26, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PawS1a Derived Peptide 20


Theoretical massNumber of molelcules
Total (without water)1,6721
Polymers1,6721
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the best MOLPROBITY score
RepresentativeModel #1structure with the best molprobity score

-
Components

#1: Protein/peptide PawS1a Derived Peptide 20


Mass: 1671.912 Da / Num. of mol.: 1 / Fragment: residues 63-78 / Source method: obtained synthetically
Details: Assembled by Fmoc solid phase peptide synthesis and cyclised by native chemical ligation.
Source: (synth.) Zinnia haageana (plant) / References: UniProt: A0A0A0V2B6

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1312D DQF-COSY
1422D 1H-13C HSQC
1512D 1H-15N HSQC

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.8 mg/mL PawS Derived Peptide 20 (PDP-20), 90% H2O/10% D2O90% H2O/10% D2O
21.8 mg/mL PawS Derived Peptide 20 (PDP-20), 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1.8 mg/mLPawS Derived Peptide 20 (PDP-20)-11
1.8 mg/mLPawS Derived Peptide 20 (PDP-20)-22
Sample conditionspH: 4 / Pressure: ambient / Temperature: 283 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CcpNMRCCPNdata analysis
CcpNMRCCPNpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: Torsion angle dynamics
NMR representativeSelection criteria: structure with the best molprobity score
NMR ensembleConformer selection criteria: structures with the best MOLPROBITY score
Conformers calculated total number: 50 / 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