- PDB-1m0g: Solution structure of the alpha domain of mt_nc -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 1m0g
Title
Solution structure of the alpha domain of mt_nc
Components
metallothionein MT_nc
Keywords
METAL BINDING PROTEIN / Cadmium-thiolate cluster
Function / homology
Function and homology information
detoxification of copper ion / intracellular zinc ion homeostasis / cellular response to zinc ion / cellular response to cadmium ion / cellular response to copper ion / positive regulation of ERK1 and ERK2 cascade / nucleus / metal ion binding / cytoplasm Similarity search - Function
Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
-
Experimental details
-
Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
2D NOESY
1
2
1
2D TOCSY
1
3
1
E-COSY
1
4
1
DQF-COSY
1
5
2
[113Cd,1H]COSY
-
Sample preparation
Details
Solution-ID
Contents
Solvent system
1
2mMmetallothoinein; 95% H2O, 5% D2O
95% H2O/5% D2O
2
2mM metallothoinein, U-113Cd; 95% H2O, 5% D2O
95% H2O/5% D2O
Sample conditions
pH: 7 / Pressure: ambient / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR
-
NMR measurement
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelength
Relative weight: 1
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Bruker AVANCE
Bruker
AVANCE
400
1
Bruker AVANCE
Bruker
AVANCE
600
2
-
Processing
NMR software
Name
Version
Developer
Classification
NMRPipe
Delaglio
processing
NMRView
4.0.3
Johnsonn
dataanalysis
DYANA
1.5
Guentert
structuresolution
DYANA
1.5
Guentert
refinement
Refinement
Method: torsion angle dynamics / Software ordinal: 1 Details: the structures are based on a total of 373 NOEs,16 Cd-S bonds and 40 dihedral angle restraints
NMR representative
Selection criteria: fewest violations
NMR ensemble
Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 20 / 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.
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