Mass: 6202.298 Da / Num. of mol.: 2 Mutation: CHAIN A: R31M,E36Y,R40L, CHAIN B: R131M,E136Y,R140L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage P22 (virus) / Genus: P22-like viruses / Gene: MUTATED ARC GENE / Plasmid: PSA300-MYL / Production host: Escherichia coli (E. coli) / Strain (production host): X90 / References: UniProt: P03050
-
Experimental details
-
Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
NOESY
1
2
1
TOCSY
1
3
1
ROESY
1
4
1
3D-NOESY-HSQC
1
5
1
3D TOCSY-HSQC
NMR details
Text: THE STRUCTURE WAS DETERMINED USING MULTI-DIMENSIONAL NMR SPECTROCOPY ON 15N LABELED ARC-MYL
-
Sample preparation
Sample conditions
Ionic strength: 50 mM KPI, 150 mM NACL / pH: 4.5 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR
-
NMR measurement
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Bruker AMX500
Bruker
AMX500
500
1
Bruker DMX600
Bruker
DMX600
600
2
-
Processing
NMR software
Name
Developer
Classification
Discover
BIOSYM
refinement
Discover
MSI, INC.
structuresolution
Refinement
Method: simulated annealing / Software ordinal: 1
NMR ensemble
Conformer selection criteria: LEAST RESTRAINT VIOLATION AND TOTAL ENERGY Conformers calculated total number: 40 / Conformers submitted total number: 14
+
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