- PDB-3cz8: Crystal structure of putative sporulation-specific glycosylase yd... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 3cz8
Title
Crystal structure of putative sporulation-specific glycosylase ydhD from Bacillus subtilis
Components
Putative sporulation-specific glycosylase ydhD
Keywords
HYDROLASE / STRUCTURAL GENOMICS / UNCHARACTERIZED PROTEIN / PROTEIN STRUCTURE INITIATIVE / PSI-2 / New York SGX Research Center for Structural Genomics / NYSGXRC / Carbohydrate metabolism / Glycosidase / Polysaccharide degradation / Sporulation
Function / homology
Function and homology information
Hydrolases; Glycosylases / spore wall / hydrolase activity, acting on glycosyl bonds / sporulation resulting in formation of a cellular spore / chitin binding / polysaccharide catabolic process Similarity search - Function
Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 17, 2008
Radiation
Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9793 Å / Relative weight: 1
Reflection
Resolution: 2.15→50 Å / Num. obs: 41723 / % possible obs: 99.9 % / Observed criterion σ(I): -0.5 / Redundancy: 5.6 % / Biso Wilson estimate: 37.4 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 5.2
Reflection shell
Resolution: 2.15→2.23 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.1 / % possible all: 99.7
-
Processing
Software
Name
Version
Classification
SHELXD
phasing
REFMAC
5.3.0034
refinement
MAR345
CCD
datacollection
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: SAD / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.78 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.24 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.25793
1212
3.1 %
RANDOM
Rwork
0.19597
-
-
-
obs
0.19787
37618
99.99 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 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