- PDB-4dlp: Crystal structure of methionyl-tRNA synthetase MetRS from Brucell... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 4dlp
Title
Crystal structure of methionyl-tRNA synthetase MetRS from Brucella melitensis bound to selenomethionine
Components
Aminoacyl-tRNA synthetase, class I:Aminoacyl-tRNA synthetase, class Ia:Methionyl-tRNA synthetase, class Ia
Keywords
LIGASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / class Ia aminoacyl-tRNA synthetase / selenomethionine / anomalous signal / protein synthesis / ATP-dependent
Function / homology
Function and homology information
methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / ATP binding / cytoplasm Similarity search - Function
A: Aminoacyl-tRNA synthetase, class I:Aminoacyl-tRNA synthetase, class Ia:Methionyl-tRNA synthetase, class Ia B: Aminoacyl-tRNA synthetase, class I:Aminoacyl-tRNA synthetase, class Ia:Methionyl-tRNA synthetase, class Ia C: Aminoacyl-tRNA synthetase, class I:Aminoacyl-tRNA synthetase, class Ia:Methionyl-tRNA synthetase, class Ia hetero molecules
Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal grow
Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: BrabA.10201.a.A1 PW27667 at 28.7 mg/mL with 5 mM selenomethionine and 5 mM ATP against JCSG+ screen condition C3, 0.2 M ammonium nitrate, 20% PEG 3350, crystal tracking ID 226820c3, pH 7.5, ...Details: BrabA.10201.a.A1 PW27667 at 28.7 mg/mL with 5 mM selenomethionine and 5 mM ATP against JCSG+ screen condition C3, 0.2 M ammonium nitrate, 20% PEG 3350, crystal tracking ID 226820c3, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
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