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Yorodumi- PDB-2vcb: Family 89 Glycoside Hydrolase from Clostridium perfringens in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vcb | ||||||
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Title | Family 89 Glycoside Hydrolase from Clostridium perfringens in complex with PUGNAc | ||||||
Components | ALPHA-N-ACETYLGLUCOSAMINIDASE | ||||||
Keywords | HYDROLASE / MUCOPOLYSACCHARIDOSIS / ALPHA-N-ACETYLGLUCOSAMINIDASE / FAMILY 89 GLYCOSIDE HYDROLASE / GH89 / NAGLU / PUGNAC / SANFILIPPO DISEASE | ||||||
Function / homology | Function and homology information hydrolase activity, acting on glycosyl bonds / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | CLOSTRIDIUM PERFRINGENS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 2.2 Å | ||||||
Authors | Ficko-Blean, E. / Stubbs, K.A. / Berg, O. / Vocadlo, D.J. / Boraston, A.B. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2008 Title: Structural and Mechanistic Insight Into the Basis of Mucopolysaccharidosis Iiib. Authors: Ficko-Blean, E. / Stubbs, K.A. / Nemirovsky, O. / Vocadlo, D.J. / Boraston, A.B. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vcb.cif.gz | 193.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vcb.ent.gz | 156 KB | Display | PDB format |
PDBx/mmJSON format | 2vcb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vc/2vcb ftp://data.pdbj.org/pub/pdb/validation_reports/vc/2vcb | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 102273.219 Da / Num. of mol.: 1 / Fragment: RESIDUES 26-916 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS (bacteria) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q0TST1, UniProt: A0A0H2YU91*PLUS, alpha-N-acetylglucosaminidase |
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#2: Chemical | ChemComp-OAN / |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.47 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 113.15 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→29.69 Å / Num. obs: 53561 / % possible obs: 90.3 % / Observed criterion σ(I): 2 / Redundancy: 2.61 % / Rmerge(I) obs: 0.07 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.833 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.285 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.68 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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