[English] 日本語
Yorodumi
- PDB-1n4n: Structure of the Plant Defensin PhD1 from Petunia Hybrida -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1n4n
TitleStructure of the Plant Defensin PhD1 from Petunia Hybrida
Componentsfloral defensin-like protein 1
KeywordsPLANT PROTEIN / Cysteine-stabilised alpha-beta motif / fifth disulfide bond
Function / homology
Function and homology information


vacuole / defense response to fungus / killing of cells of another organism / extracellular region
Similarity search - Function
Gamma-thionin family / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Floral defensin-like protein 1
Similarity search - Component
Biological speciesPetunia x hybrida (garden petunia)
MethodSOLUTION NMR / Torsion angle simulated annealing protocol, incorporated in CNS. Refinement in a box with explicit water molecules using the method of Linge, Nilges (1999)
AuthorsJanssen, B.J.C. / Schirra, H.J. / Lay, F.T. / Anderson, M.A. / Craik, D.J.
CitationJournal: Biochemistry / Year: 2003
Title: Structure of Petunia hybrida defensin 1, a novel plant defensin with five disulfide bonds
Authors: Janssen, B.J.C. / Schirra, H.J. / Lay, F.T. / Anderson, M.A. / Craik, D.J.
History
DepositionNov 1, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: floral defensin-like protein 1


Theoretical massNumber of molelcules
Total (without water)5,2221
Polymers5,2221
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 least restraint violations,structures with the lowest energy
RepresentativeModel #19lowest energy

-
Components

#1: Protein/peptide floral defensin-like protein 1 / PhD1


Mass: 5222.335 Da / Num. of mol.: 1 / Fragment: residues 1-47 / Source method: isolated from a natural source / Source: (natural) Petunia x hybrida (garden petunia) / References: UniProt: Q8H6Q1
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
1322D NOESY
142E-COSY
2512D NOESY
261DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.94mM 1H-PhD190% H2O/10% D2O
20.94mM 1H-PhD199% D2O, 1% H2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.94mM 3.1ambient 310 K
20.94mM 3.1ambient 280 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 750 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
XwinNMR2.6Brukerprocessing
CCNMRglxccExplorerCieslar & Kalusdata analysis
X-PLOR3.851Brungerstructure solution
CNS1.1Brungerstructure solution
CNS1.1Brungerrefinement
RefinementMethod: Torsion angle simulated annealing protocol, incorporated in CNS. Refinement in a box with explicit water molecules using the method of Linge, Nilges (1999)
Software ordinal: 1
Details: The structures are based on 407 NOE-derived inter-residual distance constraints, 26 phi- and 28 chi1- angle constraints, and 30 distance constraints for 15 hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
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://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