The biological assembly is a dimer, generated by applying the transformation y-x,y,-1/2-z to the fractional coordinates in the assymetric unit, or by transforming the orthogonal coordinates (in angstroms) according to -x,y,-121.0-z
-
Components
#1: Protein
thymidylatesynthase / TS / TSase
Mass: 36538.359 Da / Num. of mol.: 1 / Mutation: Y261A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus casei (bacteria) / Gene: THYA / Plasmid: pSCTS9 / Production host: Escherichia coli (E. coli) / Strain (production host): chi2913recA / References: UniProt: P00469, thymidylate synthase
Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.94 Å3/Da / Density % sol: 58.16 %
Crystal grow
Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: protein in 20mM KPO4 buffer with 15-20mM ammonium sulfate, DTT and 38mM dUMP, against 20mM KPO4 buffer alone, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 7.00
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