Mass: 2383.698 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Komagataella pastoris (fungus) / References: UniProt: P01308
#2: Protein/peptide
Insulin
Mass: 3426.894 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Komagataella pastoris (fungus) / References: UniProt: P01308
-
Experimental details
-
Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Sample state
Spectrometer-ID
Type
1
1
1
isotropic
1
4D NOESY
1
2
1
isotropic
1
3D 13C-EDITED NOESY
1
3
1
isotropic
1
3DCBCA(CO)NH
1
4
1
isotropic
1
2D 1H-15N HSQC
1
5
1
isotropic
1
2D 1H-13C HSQC
2
6
2
isotropic
1
2D 1H-1H TOCSY
2
7
2
isotropic
1
2D 1H-1H NOESY
-
Sample preparation
Details
Type
Solution-ID
Contents
Details
Label
Solvent system
solution
1
0.5mM13C, 15NB24YDKP, 90% H2O/10% D2O
B10D, B24Y, B28K, B29PINSULIN
15N, 13C_SAMPLE
90% H2O/10% D2O
solution
2
0.5mMB24DKP, 90% H2O/10% D2O
B10D, B24Y, B28K, B29PINSULIN
UNLABELED
90% H2O/10% D2O
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
0.5mM
B24YDKP
13C, 15N
1
0.5mM
B24DKP
naturalabundance
2
Sample conditions
Conditions-ID
Details
Ionic strength
Label
pH
Pressure (kPa)
Temperature (K)
1
A1-A21 AND B22-B43 13C, N15-LABELED, B24-B51 UNLABLED
0.1mM
13C, 15N
7.4
1atm
298K
2
0.1mM
UNLABELED
7.4
1atm
303K
-
NMR measurement
NMR spectrometer
Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz
-
Processing
NMR software
Name
Developer
Classification
TopSpin
BrukerBiospin
collection
X-PLOR NIH
Schwieters, Kuszewski, TjandraandClore
refinement
NMRPipe
Delaglio, Grzesiek, Vuister, Zhu, PfeiferandBax
processing
PIPP
Garrett
peakpicking
Insight II
AccelrysSoftwareInc.
dataanalysis
X-PLOR NIH
Schwieters, Kuszewski, TjandraandClore
structurecalculation
Refinement
Method: simulated annealing / Software ordinal: 2
NMR representative
Selection criteria: fewest violations
NMR ensemble
Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / 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