[English] 日本語
Yorodumi
- PDB-7m29: Solution NMR Structure of PawL-Derived Peptide PLP-29 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7m29
TitleSolution NMR Structure of PawL-Derived Peptide PLP-29
ComponentsPawL-Derived Peptide PLP-29
KeywordsPLANT PROTEIN / Cyclic / PLP / Orbitide / AEP-processed
Biological speciesSteirodiscus tagetes (plant)
MethodSOLUTION NMR / simulated annealing
AuthorsPayne, C.D. / Rosengren, K.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP190102058 Australia
CitationJournal: J.Nat.Prod. / Year: 2021
Title: Structural Characterization of the PawL-Derived Peptide Family, an Ancient Subfamily of Orbitides.
Authors: Payne, C.D. / Fisher, M.F. / Mylne, J.S. / Rosengren, K.J.
History
DepositionMar 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Database references / Category: citation / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Dec 8, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PawL-Derived Peptide PLP-29


Theoretical massNumber of molelcules
Total (without water)8531
Polymers8531
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: Monomeric structure is fully consistent with NOESY data
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the least restraint violations
RepresentativeModel #1closest to the average

-
Components

#1: Protein/peptide PawL-Derived Peptide PLP-29


Mass: 852.931 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Steirodiscus tagetes (plant)

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
311isotropic12D 1H-1H NOESY
321isotropic12D 1H-1H TOCSY
331isotropic12D 1H-13C HSQC
341isotropic12D 1H-15N HSQC
151isotropic12D 1H-1H TOCSY
281isotropic12D 1H-1H TOCSY
471isotropic12D 1H-1H TOCSY
561isotropic12D 1H-1H TOCSY

-
Sample preparation

DetailsType: solution / Contents: 4 mg/mL PLP-29, 99.5% CD3CN / Label: PLP-29 / Solvent system: 99.5% CD3CN
SampleConc.: 4 mg/mL / Component: PLP-29 / Isotopic labeling: natural abundance
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
10 mM288K3.5 1 atm288 K
20 mM293K3.5 1 atm293 K
30 mM298K3.5 1 atm298 K
40 mM303K3.5 1 atm298 K
50 mM308K3.5 1 atm298 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 900 MHz

-
Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
Refinement
MethodSoftware ordinalDetails
simulated annealing5using torsion angle dynamics
simulated annealing2using torsion angle dynamics and Cartesian space
simulated annealing1minimized in explicit water using Cartesian dynamics
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
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