NO RESTRAINT VIOLATIONS LESS THAN 0.2 ANGSTROMS AND MIMINUM ENERGY LESS THAN 115.0 KCAL/MOL BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE: 1
Representative
Model #1
minimized average structure
-
Components
#1: Protein
NeurotoxinCn11 / CN12
Mass: 7154.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: TOXIN OBTAINED DIRECTLY FROM VENOM OF CENTRUROIDES NOXIUS. ACTIVITY IS VERY LOW, HOWEVER CN12 HAS SOME REQUIREMENTS FOR BEING A VERY ACTIVE TOXIN. Source: (natural) Centruroides noxius (Mexican scorpion) / Secretion: VENOM / References: UniProt: P63019
-
Experimental details
-
Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
DQF COSY, 2D TOCSY, AND 2D NOSEY
2
2
2
DQF-COSY, 2D TOCSY, AND 2D NOESY
NMR details
Text: THE STRUCTURE WAS DETERMINED USING HOMONUCLEAR 1H-1H 2D NMR ON THE NATURAL TOXIN EXTRACTED FROM THE SCORPION VENOM
-
Sample preparation
Details
Solution-ID
Contents
Solvent system
1
0.6mMinH2O/D2O90:10%;
90% H2Oand10% D2O
2
0.6mMin100% D2O
100% D2O
Sample conditions
Conditions-ID
Ionic strength
pH
Pressure (kPa)
Temperature (K)
1
none
3.1
ambient
300K
2
none
3.1
ambient
300K
-
NMR measurement
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Conformer selection criteria: NO RESTRAINT VIOLATIONS LESS THAN 0.2 ANGSTROMS AND MIMINUM ENERGY LESS THAN 115.0 KCAL/MOL BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE: 1 Conformers calculated total number: 250 / Conformers submitted total number: 19
+
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.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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
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