structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations
Representative
-
Components
#1: Protein
Ribonuclease / Gp61.9
Mass: 17939.549 Da / Num. of mol.: 1 / Mutation: H48A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: regB, 61.9 / Plasmid: pTOXR(RegB-H48A) / Production host: Escherichia coli (E. coli) / Strain (production host): BL31(DE3) References: UniProt: P13312, Hydrolases; Acting on ester bonds
-
Experimental details
-
Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
HNCO
1
2
1
HNCA
1
3
1
HN(CO)CA
1
4
1
HN(CA)CB
1
5
1
CBCA(CO)NH
1
6
2
(H)CCH-TOCSY
1
7
2
3D 13C-separated NOESY
1
8
3
3D 15N-separated NOESY
1
9
4
2D NOESY
1
10
4
2D TOCSY
1
11
4
2D COSY
-
Sample preparation
Details
Solution-ID
Contents
Solvent system
1
Uniform labeling with 13C, 15N (U-80% 13C, U-100% 15N)
90% H2O, 10% D20
2
Uniform labeling with 13C, 15N (U-80% 13C, U-100% 15N)
100% D2O
3
Uniform labeling with 15N (U-100% 15N)
90% H2O/10% D2O
4
Uniform labeling with 15N (U-100% 15N)
100% D2O
Sample conditions
Ionic strength: 50 mM citrate, 300 mM NaCl, 20 mM DTT / pH: 6.0 / Pressure: ambient / Temperature: 305 K
-
NMR measurement
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelength
Relative weight: 1
NMR spectrometer
Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz
-
Processing
NMR software
Name
Version
Developer
Classification
XwinNMR
3.5
BRUKER
processing
Sparky
3.11
GoddardT.D. andKnellerD.G.
dataanalysis
INCA
1
GilquinB.
structuresolution
INCA
1
GilquinB.
refinement
Refinement
Method: mix of manual, automatic NOE assignment procedure / Software ordinal: 1
NMR ensemble
Conformer selection criteria: structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations Conformers calculated total number: 30 / Conformers submitted total number: 15
+
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