- PDB-8apz: Crystal structure of wild-type L-N-Carbamoylase from Sinorhizobiu... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 8apz
Title
Crystal structure of wild-type L-N-Carbamoylase from Sinorhizobium meliloti
Components
N-carbamoyl-L-amino-acid hydrolase
Keywords
HYDROLASE / peptidase family M20/M25/M40
Function / homology
Function and homology information
N-carbamoyl-L-amino-acid hydrolase / N-carbamoyl-L-amino-acid hydrolase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines / amino acid biosynthetic process / metal ion binding Similarity search - Function
Method to determine structure: MOLECULAR REPLACEMENT Starting model: AF model Resolution: 1.75→43.22 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.916 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1855
3687
4.9 %
RANDOM
Rwork
0.1495
-
-
-
obs
0.1513
70922
99.46 %
-
Solvent computation
Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
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