- PDB-2wvs: Crystal structure of an alpha-L-fucosidase GH29 trapped covalent ... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2wvs
Title
Crystal structure of an alpha-L-fucosidase GH29 trapped covalent intermediate from Bacteroides thetaiotaomicron in complex with 2- fluoro-fucosyl fluoride using an E288Q mutant
Components
ALPHA-L-FUCOSIDASE
Keywords
HYDROLASE / ALPHA-L-FUCOSE / GLYCOSIDE HYDROLASE FAMILY 29
Function / homology
Function and homology information
alpha-L-fucosidase activity / fucose metabolic process / glycoside catabolic process / lysosome Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 922 / Source method: isolated from a natural source / Formula: H2O
Compound details
ENGINEERED RESIDUE IN CHAIN A, GLU 288 TO GLN ENGINEERED RESIDUE IN CHAIN B, GLU 288 TO GLN ...ENGINEERED RESIDUE IN CHAIN A, GLU 288 TO GLN ENGINEERED RESIDUE IN CHAIN B, GLU 288 TO GLN ENGINEERED RESIDUE IN CHAIN C, GLU 288 TO GLN ENGINEERED RESIDUE IN CHAIN D, GLU 288 TO GLN
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→97.56 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.921 / SU B: 6.166 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.288 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES REFINED INDIVIDUALLY. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.235
4816
5 %
RANDOM
Rwork
0.178
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obs
0.181
91482
96.8 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK