Mass: 2423.721 Da / Num. of mol.: 1 / Fragment: sequence database residues 183-204 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human). References: UniProt: Q13153, EC: 2.7.1.37
-
Experimental details
-
Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
3D 15N-separated NOESY
2
2
2
3D 13C-separated NOESY
2
3
2
13C,15N-filtered, 13C-separated NOESY
-
Sample preparation
Details
Solution-ID
Contents
Solvent system
1
1mM 15N labelled PIX-SH3 complexed with 1.2 mM peptide in 20 mM Na2HPO4/NaH2PO4, pH 7.3, 100mM Na2SO4, 0.05% NaN3, 90% H2O, 10% D2O
90% H2O/10% D2O
2
1mM 15N,13C labelled PIX-SH3 complexed with 1.2 mM peptide in 20 mM Na2HPO4/NaH2PO4, pH 7.3, 100mM Na2SO4, 0.05% NaN3, 90% H2O, 10% D2O
90% H2O/10% D2O
Sample conditions
Conditions-ID
Ionic strength
pH
Pressure (kPa)
Temperature (K)
1
100mMNa2SO4
7.3
1atm
298K
2
100mMNa2SO4
7.3
1atm
298K
-
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 DRX
Bruker
DRX
600
1
Bruker DRX
Bruker
DRX
800
2
-
Processing
NMR software
Name
Version
Developer
Classification
XwinNMR
2.6
Bruker
collection
Azara
2.7
Boucher
processing
ANSIG
3.3
Kraulis
dataanalysis
ARIA
1.2
Linge & Nilges
structuresolution
CNS
1.1
Brungeretal
structuresolution
CNS
1.1
Brungeretal
refinement
Refinement
Method: simluated annealing with torsion angle dynamics, Cartesian dynamics cooling Software ordinal: 1 Details: Total of 1788 unambiguous and 761 ambiguous NOE derieved distance restraints, 33 dihedral angle restraints.
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: 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