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Yorodumi- PDB-2j47: Bacteroides thetaiotaomicron GH84 O-GlcNAcase in complex with a i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2j47 | ||||||
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Title | Bacteroides thetaiotaomicron GH84 O-GlcNAcase in complex with a imidazole-pugnac hybrid inhibitor | ||||||
Components | GLUCOSAMINIDASE | ||||||
Keywords | INHIBITOR / O-GLCNACASE / IMIDAZOLE / GH84 / PUGNAC / ENZYME / INHIBITION | ||||||
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 | ||||||
Biological species | BACTEROIDES THETAIOTAOMICRON (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Dennis, R.J. / Davies, G.J. | ||||||
Citation | Journal: Chem. Commun. / Year: 2006 Title: Inhibition of O-Glcnacase by a Gluco-Configured Nagstatin and a Pugnac-Imidazole Hybrid Inhibitor Authors: Shanmugasundaram, B. / Debowski, A.W. / Dennis, R.J. / Davies, G.J. / Vocadlo, D.J. / Vasella, A. #1: Journal: Nat.Struct.Mol.Biol. / Year: 2006 Title: Structure and Mechanism of a Bacterial Beta-Glucosaminidase Having O-Glcnacsae Activity Authors: Dennis, R.J. / Taylor, E.J. / Macauley, M.S. / Stubbs, K.A. / Turkenburg, J.P. / Hart, S.J. / Black, G.N. / Vocadlo, D.J. / Davies, G.J. | ||||||
History |
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Remark 700 | 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2j47.cif.gz | 139.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j47.ent.gz | 106.4 KB | Display | PDB format |
PDBx/mmJSON format | 2j47.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/2j47 ftp://data.pdbj.org/pub/pdb/validation_reports/j4/2j47 | HTTPS FTP |
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-Related structure data
Related structure data | 2choS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 82316.109 Da / Num. of mol.: 1 / Fragment: RESIDUES 22-737 Source method: isolated from a genetically manipulated source Details: PUGNAC-IMIDAZOLE HYBRID INHIBITOR Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria) Strain: VPI-5482 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q89ZI2, beta-N-acetylhexosaminidase |
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#2: Chemical | ChemComp-GDV / ( |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Sequence details | SIGNAL PETIDE FROM RESIDUE 1-22. SEQUENCE CLONED FROM N23. NUMBERED IN PDB AS IN MATURE PROTEIN, ...SIGNAL PETIDE FROM RESIDUE 1-22. SEQUENCE CLONED FROM N23. NUMBERED IN PDB AS IN MATURE PROTEIN, GLN 1, ASN 2, ETC. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49 % |
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Crystal grow | pH: 6 Details: 0.6M SODIUM ACETATE,13% (V/V) PEG3500, 0.1M MES PH6.0, 10% (V/V) GLYCEROL, pH 6.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→50 Å / Num. obs: 53713 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.97→2.04 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CHO Resolution: 1.98→92.85 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.06 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.141 / 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: 26.14 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→92.85 Å
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Refine LS restraints |
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