[English] 日本語
Yorodumi
- PDB-1ixt: Structure of a Novel P-Superfamily Spasmodic Conotoxin Reveals an... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ixt
TitleStructure of a Novel P-Superfamily Spasmodic Conotoxin Reveals an Inhibitory Cystine Knot Motif
Componentsspasmodic protein tx9a-like protein
KeywordsTOXIN / conotoxin / P-superfamily / ICK / inhibitory cystine knot / spasmodic / Conus gloriamaris / gm9a / gm9.1
Function / homologySpasmodic peptide gm9a / Spasmodic peptide gm9a; conotoxin from Conus species / toxin activity / extracellular region / Conotoxin Gm9.1
Function and homology information
MethodSOLUTION NMR / CNS, minimized in water
AuthorsMiles, L.A. / Dy, C.Y. / Nielsen, J. / Barnham, K.J. / Hinds, M.G. / Olivera, B.M. / Bulaj, G. / Norton, R.S.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Structure of a Novel P-Superfamily Spasmodic Conotoxin Reveals an Inhibitory Cystine Knot Motif
Authors: Miles, L.A. / Dy, C.Y. / Nielsen, J. / Barnham, K.J. / Hinds, M.G. / Olivera, B.M. / Bulaj, G. / Norton, R.S.
History
DepositionJul 4, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: spasmodic protein tx9a-like protein


Theoretical massNumber of molelcules
Total (without water)2,8081
Polymers2,8081
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200back calculated data agree with experimental NOESY spectrum,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein/peptide spasmodic protein tx9a-like protein


Mass: 2808.098 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-27 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Conus gloriamaris (Eukaryota).
References: UniProt: Q9GU57

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
131E-COSY
141TOCSY

-
Sample preparation

DetailsContents: gm9a peptide / Solvent system: 90% H20, 10% D20
Sample conditionsIonic strength: NA / pH: 5.5 / Pressure: 1 atmosphere / Temperature: 278 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker DRXBrukerDRX6002

-
Processing

NMR softwareName: XwinNMR / Version: 1.3 / Developer: Bruker / Classification: collection
RefinementMethod: CNS, minimized in water / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 200 / 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