- PDB-8ka2: Crystal structure of the RID-dependent transforming NADase domain... -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 8ka2
Title
Crystal structure of the RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) from Vibrio vulnificus
Components
RDTND-RID CBD
Keywords
TOXIN / MARTX toxin / RDTND-RID / NADase
Function / homology
Function and homology information
Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / host cell cytosol / acyltransferase activity / ligase activity / cysteine-type peptidase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding / host cell plasma membrane ...Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / host cell cytosol / acyltransferase activity / ligase activity / cysteine-type peptidase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding / host cell plasma membrane / proteolysis / extracellular region / membrane / metal ion binding Similarity search - Function
the Korea Research Institute of Bioscience and Biotechnology (KRIBB) Research Initiative Program(KGM1382312)
Other government
the Korea Research Institute of Bioscience and Biotechnology (KRIBB) Research Initiative Program(KGM2112335)
Citation
Journal: To Be Published Title: Crystal structure of the RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) from Vibrio vulnificus Authors: Lee, Y. / Choi, S. / Hwang, J. / Kim, M.H.
Method to determine structure: SAD / Resolution: 3.38→40.42 Å / Cor.coef. Fo:Fc: 0.814 / Cor.coef. Fo:Fc free: 0.764 / Cross valid method: THROUGHOUT / ESU R Free: 0.735 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.32212
830
5.2 %
RANDOM
Rwork
0.28599
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obs
0.28789
15125
82.79 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK