[English] 日本語
Yorodumi
- PDB-1zrx: solution structure of stomoxyn in H20/TFE 50% -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1zrx
Titlesolution structure of stomoxyn in H20/TFE 50%
Componentsstomoxyn
KeywordsANTIMICROBIAL PROTEIN / ANTIBIOTIC / helical peptide in TFE
Function / homology
Function and homology information


defense response to fungus / xenobiotic metabolic process / killing of cells of another organism / defense response to bacterium / innate immune response / extracellular region
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #280 / Stomoxyn / Insect antimicrobial peptide, stomoxyn / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
MethodSOLUTION NMR / molecular dynamics
AuthorsLandon, C. / Meudal, H. / Boulanger, N. / Bulet, P. / Vovelle, F.
Citation
Journal: Biopolymers / Year: 2006
Title: Solution structures of stomoxyn and spinigerin, two insect antimicrobial peptides with an alpha-helical conformation.
Authors: Landon, C. / Meudal, H. / Boulanger, N. / Bulet, P. / Vovelle, F.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: Insect immunity. Constitutive expression of a cysteine-rich antifungal and a linear antibacterial peptide in a termite insect
Authors: Lamberty, M. / Zachary, D. / Lanot, R. / Bordereau, C. / Robert, A. / Hoffmann, J.A. / Bulet, P.
History
DepositionMay 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: stomoxyn


Theoretical massNumber of molelcules
Total (without water)4,4271
Polymers4,4271
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)10 / 100structures with the lowest energy and the least restraint violations
RepresentativeModel #1representative conformer

-
Components

#1: Protein/peptide stomoxyn


Mass: 4427.179 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: solid-phase synthesis (Boc). Sequence occurs naturally in Stomoxys calcitrans, Stable fly
References: UniProt: Q8T9R8

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D TOCSY
1312D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

-
Sample preparation

DetailsContents: 2mM stomoxyn / Solvent system: 50% H2O, 50% TFE
Sample conditionspH: 5.3 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Bcollection
NMRPipe2002.044.17.08Delaglioprocessing
NMRView5.0.16Johnsondata analysis
ARIA1.1Lingestructure solution
CNS1.1Brungerstructure solution
CNS1.1Brungerrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: the structures are based on a total of 739 distance NOE-derived restraints
NMR representativeSelection criteria: representative conformer
NMR ensembleConformer selection criteria: structures with the lowest energy and the least restraint violations
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://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