- PDB-2h3g: Structure of the Type III Pantothenate Kinase (CoaX) from Bacillu... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 2h3g
Title
Structure of the Type III Pantothenate Kinase (CoaX) from Bacillus Anthracis
Components
BIOSYNTHETIC PROTEIN
Keywords
BIOSYNTHETIC PROTEIN / pantothenate kinase / bacillus anthracis / anthrax / type III pantothenate kinase / CoaX / CoaA / ASKHA
Function / homology
Function and homology information
pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / ATP binding / metal ion binding / cytoplasm Similarity search - Function
Type III pantothenate kinase / Type III pantothenate kinase / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology
The biological assembly is a dimer generated from the monomer in the asymmetric unit by crystallographic symmetry and interacting mainly through residues 147-161 and 179-203.
-
Components
#1: Protein
BIOSYNTHETICPROTEIN
Mass: 29957.629 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis str. (bacteria) / Species: Bacillus anthracis / Strain: Ames / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q73FE2, UniProt: Q81VX4*PLUS
Mass: 18.015 Da / Num. of mol.: 180 / 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: 3.19 Å3/Da / Density % sol: 61.5 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: protein buffer: 10 mM Na HEPES pH 7.5, 10 mM KCl protein concentration: 22.5-25.0 mg/mL reservoir solution: 24-26% ethylene glycol reservoir volume: 0.5 mL drop volume: 2 + 2 uL or 4 + 4 uL, ...Details: protein buffer: 10 mM Na HEPES pH 7.5, 10 mM KCl protein concentration: 22.5-25.0 mg/mL reservoir solution: 24-26% ethylene glycol reservoir volume: 0.5 mL drop volume: 2 + 2 uL or 4 + 4 uL, protein + reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Av σ(I) over netI: 14.9 / Number: 161979 / Rmerge(I) obs: 0.05 / Χ2: 0.82 / D res high: 2.1 Å / D res low: 44.53 Å / Num. obs: 22637 / % possible obs: 99.9 / Redundancy: 7.1 %
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