Mass: 7458.308 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Residues 1-4 (GSHM) are from the expression tag. / Source: (gene. exp.) Homo sapiens (human) / Gene: CASKIN1, KIAA1306 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WXD9
-
Experimental details
-
Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Sample state
Spectrometer-ID
Type
1
1
4
isotropic
1
2D 1H-15N HSQC
1
2
4
isotropic
1
3D HN(CA)CB
1
3
4
isotropic
1
3DCBCA(CO)NH
1
4
4
isotropic
1
3DHBHA(CO)NH
1
5
4
isotropic
1
3D CC-TOCSY-NNH
1
6
4
isotropic
1
3D HCC-TOCSY
1
7
4
isotropic
1
3D (H)CCH-TOCSY
1
8
4
isotropic
1
2D 1H-13C HSQC aliphatic
1
9
4
isotropic
1
2D 1H-13C HSQC aromatic
1
10
5
isotropic
1
2D 1H-15N HSQC
1
11
5
isotropic
1
2D 1H-15N HSQC NH2 only
1
12
5
isotropic
1
3D 1H-15N NOESY
1
13
4
isotropic
1
3D 1H-13C NOESY aliphatic
1
14
4
isotropic
1
3D 1H-13C NOESY aromatic
1
15
4
isotropic
1
3D Met-Met NOESY
1
16
6
isotropic
1
2D 1H-1H NOESY
-
Sample preparation
Details
Type
Solution-ID
Contents
Details
Label
Solvent system
solution
4
0.6 mM [U-13C; U-15N] human caskin1 SH3 domain, 90% H2O/10% D2O
20 mM K-phosphate, 100 mM KCl, 0.05% NaN3, 0.1 mM TCEP, pH 7.2
13C_15N_sample
90% H2O/10% D2O
solution
5
0.6 mM [U-15N] human caskin1 SH3 domain, 90% H2O/10% D2O
20 mM K-phosphate, 100 mM KCl, 0.05% NaN3, 0.1 mM TCEP, pH 7.2
15N_sample
90% H2O/10% D2O
solution
6
1mMhumancaskin1SH3domain, 90% H2O/10% D2O
20 mM K-phosphate, 100 mM KCl, 0.05% NaN3, 0.1 mM TCEP, pH 7.2
unlabeled_sample
90% H2O/10% D2O
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
0.6mM
humancaskin1SH3domain
[U-13C; U-15N]
4
0.6mM
humancaskin1SH3domain
[U-15N]
5
1mM
humancaskin1SH3domain
naturalabundance
6
Sample conditions
Details: 20 mM K-phosphate, 100 mM KCl, 0.05% NaN3, 0.1 mM TCEP, pH 7.2 Ionic strength: 20 mM K-phosphate, 100 mM KCl, 0.05% NaN3, 0.1 mM TCEP Not defined Label: condition_1 / pH: 7.2 / PH err: 0.1 / Pressure: 1 atm / Temperature: 283 K / Temperature err: 0.1
-
NMR measurement
NMR spectrometer
Type: Varian Uniform NMR System / Manufacturer: Varian / Model: Uniform NMR System / Field strength: 600 MHz
-
Processing
NMR software
Name
Developer
Classification
VnmrJ
Varian
collection
Felix
AccelrysSoftwareInc.
chemicalshiftassignment
Felix
AccelrysSoftwareInc.
peakpicking
ARIA
Linge, O'DonoghueandNilges
structurecalculation
ARIA
Linge, O'DonoghueandNilges
refinement
Refinement
Method: simulated annealing / Software ordinal: 5 Details: torsional angle simulated annealing followed by torsional angle and Cartesian molecular dynamics cooling stages
NMR representative
Selection criteria: lowest energy
NMR ensemble
Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 30
+
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