- PDB-5hbn: ClpC N-terminal domain with bound phospho-arginine -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 5hbn
Title
ClpC N-terminal domain with bound phospho-arginine
Components
Negative regulator of genetic competence ClpC/MecB
Keywords
HYDROLASE / Clp protease / degradation tag / protein phosphorylation / phospho-residue binding site
Function / homology
Function and homology information
establishment of competence for transformation / cellular response to heat / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function
Double Clp-N motif / Clp, N-terminal domain / UVR domain / UVR domain profile. / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain ...Double Clp-N motif / Clp, N-terminal domain / UVR domain / UVR domain profile. / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / Clp repeat (R) domain profile. / Clp, repeat (R) domain / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 40 / 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: 1.8 Å3/Da / Density % sol: 31.61 %
Crystal grow
Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5 Details: The optimized crystallization solution contained 13.5% w/w polyethylene glycol 4000, 500 mM ammonium sulphate, and 100 mM sodium acetate at pH 5. Hexagonal crystals of space group P 6(5) ...Details: The optimized crystallization solution contained 13.5% w/w polyethylene glycol 4000, 500 mM ammonium sulphate, and 100 mM sodium acetate at pH 5. Hexagonal crystals of space group P 6(5) formed overnight at 19C and were cryo-protected in 40% polyethylene glycol 400, 20 mM Tris pH 8, and 6 mM pArgAA prior to being flash-frozen.
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