[English] 日本語
Yorodumi
- PDB-1wt8: Solution Structure of BmP08 from the Venom of Scorpion Buthus mar... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1wt8
TitleSolution Structure of BmP08 from the Venom of Scorpion Buthus martensii Karsch, 20 structures
ComponentsNeurotoxin BmK X
KeywordsTOXIN / ALPHA/BETA scaffold
Function / homologyKnottin, scorpion toxin-like superfamily / extracellular region / Neurotoxin BmP08
Function and homology information
Biological speciesMesobuthus martensii (Chinese scorpion)
MethodSOLUTION NMR / distance geometry
AuthorsWu, H. / Chen, X. / Tong, X. / Li, Y. / Zhang, N. / Wu, G.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2005
Title: Solution structure of BmP08, a novel short-chain scorpion toxin from Buthus martensi Karsch.
Authors: Chen, X. / Li, Y. / Tong, X. / Zhang, N. / Wu, G. / Zhang, Q. / Wu, H.
History
DepositionNov 17, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 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: 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 23, 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: Neurotoxin BmK X


Theoretical massNumber of molelcules
Total (without water)3,3341
Polymers3,3341
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 / 200structures with the lowest energy
RepresentativeModel #2lowest energy

-
Components

#1: Protein/peptide Neurotoxin BmK X


Mass: 3333.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mesobuthus martensii (Chinese scorpion) / Secretion: venom / References: UniProt: Q7Z0H4
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY, 2D TOCSY, DQF-COSY
1222D NOESY, 2D TOCSY, DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

-
Sample preparation

Details
Solution-IDContentsSolvent system
13.3mM90% H2O/10% D2O
23.3mM100% D2O
Sample conditionspH: 3.02 / Pressure: ambient / Temperature: 303 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1BMike Carlisle, Dan Steele, Mike Millercollection
VNMR6.1BMike Carlisle, Dan Steele, Mike Millerprocessing
XEASY1994Tai-he Xia, Christian Barteldata analysis
DYANA1.5Peter Guntert, Christian Mumenthaler, Torsten Herrmannstructure solution
Amber5refinement
RefinementMethod: distance geometry / Software ordinal: 1
Details: The structure are based on a total of 329 constraints, 296 are NOE-derived distance constraints, 10 dihedral angle constraints, 23 distance constraints from seven hydrogen bonds and three disulfide bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 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