Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
Sequence details
AUTHORS STATE THAT THESE RESIDUES ARE ARTIFICIAL ONES THAT WERE INSERTED AS LINKER TO ENABLE THE ...AUTHORS STATE THAT THESE RESIDUES ARE ARTIFICIAL ONES THAT WERE INSERTED AS LINKER TO ENABLE THE CYCLIZATION OF THIS SMALL GAMMA-DOMAIN.
-
Experimental details
-
Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
2D 1H-1H TOCSY
1
2
1
2D 1H-1H NOESY
1
3
1
2D 1H-113Cd HSQC
2
4
1
2D 1H-1H TOCSY
2
5
1
2D 1H-1H NOESY
2
6
1
2D 1H-113Cd HSQC
-
Sample preparation
Details
Contents: 0.9 mM cyc-gEc1, 1.8 mM 113Cd CADMIUM ION, 10 mM [U-99% 2H] TRIS, 10 mM sodium perchlorate, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
0.9mM
cyc-gEc1-1
1
1.8mM
CADMIUM ION-2
113Cd
1
10mM
TRIS-3
[U-99% 2H]
1
10mM
sodium perchlorate-4
1
Sample conditions
Conditions-ID
Ionic strength
pH
Pressure (kPa)
Temperature (K)
1
0.02
7.5
ambient
307.2K
2
0.02
7.5
ambient
295.5K
-
NMR measurement
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Bruker Avance
Bruker
AVANCE
700
1
Bruker Avance
Bruker
AVANCE
600
2
Bruker DRX
Bruker
DRX
500
3
-
Processing
NMR software
Name
Version
Developer
Classification
CARA
1.9.0
KellerandWuthrich
chemicalshiftassignment
CARA
1.9.0
KellerandWuthrich
peakpicking
CARA
1.9.0
KellerandWuthrich
dataanalysis
CYANA
3.1
Guntert, MumenthalerandWuthrich
structuresolution
Sparky
3.113
Goddard
chemicalshiftassignment
Sparky
3.113
Goddard
peakpicking
Sparky
3.113
Goddard
dataanalysis
XEASY
1.3.13
Bartelsetal.
dataanalysis
XEASY
1.3.13
Bartelsetal.
peakpicking
X-PLOR NIH
2.33
Schwieters, Kuszewski, TjandraandClore
structuresolution
X-PLOR NIH
2.33
Schwieters, Kuszewski, TjandraandClore
refinement
TopSpin
3
BrukerBiospin
processing
TopSpin
3
BrukerBiospin
collection
PSVS
BhattacharyaandMontelione
validation
Refinement
Method: molecular dynamics, simulated annealing / Software ordinal: 1 Details: RESTRAINT REFINEMENT IN EXPLICIT SOLVENT (WATER), IN TORSION COORDINATES USING NOEASSIGN ALGORITHM
NMR constraints
NOE constraints total: 201 / NOE long range total count: 21 / NOE medium range total count: 38
NMR representative
Selection criteria: closest to the average
NMR ensemble
Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20
NMR ensemble rms
Distance rms dev: 0.8 Å
+
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