- PDB-8r06: CRYSTAL STRUCTURE OF THERMOANAEROBACTERIUM XYLANOLYTICUM GH116 BE... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 8r06
Title
CRYSTAL STRUCTURE OF THERMOANAEROBACTERIUM XYLANOLYTICUM GH116 BETA-GLUCOSIDASE WITH A COVALENTLY BOUND CYCLOPHELLITOL AZIRIDINE
Components
Glucosylceramidase
Keywords
HYDROLASE / Glucosylceramidase
Function / homology
Function and homology information
glucosylceramidase / glucosylceramide catabolic process / glucosylceramidase activity / beta-glucosidase activity / carbohydrate metabolic process / membrane / metal ion binding Similarity search - Function
Glycosyl-hydrolase family 116, catalytic region / Beta-glucosidase GBA2-type / Glycosyl-hydrolase family 116, N-terminal / Glycosyl-hydrolase family 116, catalytic region / beta-glucosidase 2, glycosyl-hydrolase family 116 N-term / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. Similarity search - Domain/homology
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→60.81 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.048 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE LIGAND IS COVALENTLY BOUND, ALTHOUGH THE DIFFERENCE DENSITY MAY INDICATE A SMALL PROPORTION OF AN UNREACTED FORM OF THE LIGAND, NOT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE LIGAND IS COVALENTLY BOUND, ALTHOUGH THE DIFFERENCE DENSITY MAY INDICATE A SMALL PROPORTION OF AN UNREACTED FORM OF THE LIGAND, NOT MODELLED, ALSO PRESENT IN THE ACTIVE SITE.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.18877
4366
5 %
RANDOM
Rwork
0.15457
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obs
0.15626
83288
99.19 %
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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