- PDB-2chn: Bacteroides thetaiotaomicron hexosaminidase with O-GlcNAcase acti... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2chn
Title
Bacteroides thetaiotaomicron hexosaminidase with O-GlcNAcase activity- NAG-thiazoline complex
Components
(GLUCOSAMINIDASE) x 2
Keywords
HYDROLASE / O-GLCNACASE / N-ACETYLGLUCOSAMIBE
Function / homology
Function and homology information
protein O-GlcNAcase / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / protein deglycosylation / beta-N-acetylglucosaminidase activity / carbohydrate metabolic process / identical protein binding Similarity search - Function
SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.
Mass: 18.015 Da / Num. of mol.: 1103 / Source method: isolated from a natural source / Formula: H2O
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Details
Sequence details
RESIDUES IN DISORDERED C TERMINUS MODELLED AS POLYALANINE CHAINS C AND D ARE THE UNKNOWN RESIDUES ...RESIDUES IN DISORDERED C TERMINUS MODELLED AS POLYALANINE CHAINS C AND D ARE THE UNKNOWN RESIDUES OF THE C TERMINUS OF CHAINS A AND B
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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: 2.76 Å3/Da / Density % sol: 55.1 %
Crystal grow
pH: 6 Details: 0.5M NA ACETATE, 15% PEG 3500, 0.1M MES PH6, 20% GLYCEROL, pH 6.00
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9795 Å / Relative weight: 1
Reflection
Resolution: 1.95→50 Å / Num. obs: 117950 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12
Reflection shell
Resolution: 1.95→2 Å / Redundancy: 4 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3 / % possible all: 97
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Processing
Software
Name
Version
Classification
REFMAC
5.2.0019
refinement
MOSFLM
datareduction
SCALA
datascaling
Refinement
Method to determine structure: SAD / Resolution: 1.95→39.84 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.849 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.226
6255
5 %
RANDOM
Rwork
0.185
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obs
0.187
117960
96.7 %
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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