structures with the least restraint violations,structures with the lowest energy
Representative
Model #4
fewest violations
-
Components
#1: Protein
alpha-Bungarotoxin / LONG NEUROTOXIN 1
Mass: 8005.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bungarus multicinctus (many-banded krait) / References: UniProt: P60615
-
Experimental details
-
Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
NOESY
1
2
1
DQF-COSY
2
3
2
E-COSY
NMR details
Text: This structure was determined using standard 2D homonuclear techniques.
-
Sample preparation
Details
Solution-ID
Contents
Solvent system
1
4mM alpha-Bungarotoxin pH 5.79 at 288, 298, and 308 degrees K
95% H2O/5% D2O
2
4mM alpha-Bungarotoxin pH 5.79
99.9% D2O
Sample conditions
Conditions-ID
Ionic strength
pH
Pressure (kPa)
Temperature (K)
1
nobuffers, pHadjustedw/HClandNaOH
5.79
ambient
298K
2
nobuffers, pHadjustedw/DClandNaOD
5.79
ambient
308K
-
NMR measurement
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelength
Relative weight: 1
NMR spectrometer
Type: GE GN / Manufacturer: GE / Model: GN / Field strength: 500 MHz
-
Processing
NMR software
Name
Version
Developer
Classification
MARDIGRAS
2
Borgias, B. A., andJames, T. L.
iterativematrixrelaxation
VEMBED
1
Kuntz, I. D., Thomason, J. F., andOshiro, C. M.
structuresolution
GROMOS
874Dversion
vanSchaik, R. C., andvanGunsteren, W. F.
refinement
Refinement
Method: distance geometry, molecular dynamics, matrix relaxation Software ordinal: 1 Details: total number of restraints used: 657, Total number of NOE restraints: 588, Total number of dihedral angle restraints: 60, Used 9 hydrogen-bond restraints
NMR representative
Selection criteria: fewest violations
NMR ensemble
Conformer selection criteria: structures with the least restraint violations,structures with the lowest energy Conformers calculated total number: 20 / Conformers submitted total number: 13
+
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