+Open data
-Basic information
Entry | Database: PDB / ID: 2wzh | ||||||
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Title | BtGH84 D242N in complex with MeUMB-derived oxazoline | ||||||
Components | O-GLCNACASE BT_4395 | ||||||
Keywords | HYDROLASE / GLYCOSIDE HYDROLASE / INHIBITOR / GLYCOSIDASE | ||||||
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 VPI-5482 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | He, Y. / Davies, G.J. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2010 Title: Visualizing the Reaction Coordinate of an O-Glcnac Hydrolase Authors: He, Y. / Macauley, M.S. / Stubbs, K.A. / 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 | 2wzh.cif.gz | 261.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wzh.ent.gz | 208.1 KB | Display | PDB format |
PDBx/mmJSON format | 2wzh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wzh_validation.pdf.gz | 448.9 KB | Display | wwPDB validaton report |
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Full document | 2wzh_full_validation.pdf.gz | 451.8 KB | Display | |
Data in XML | 2wzh_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 2wzh_validation.cif.gz | 34.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wz/2wzh ftp://data.pdbj.org/pub/pdb/validation_reports/wz/2wzh | HTTPS FTP |
-Related structure data
Related structure data | 2wziC 2x0hC 2choS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 84586.938 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON VPI-5482 (bacteria) Plasmid: YSBLLICPET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q89ZI2, beta-N-acetylhexosaminidase |
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#2: Chemical | ChemComp-NGO / |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.41 % / Description: NONE |
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Crystal grow | Details: 0.2M SODIUM MALONATE, 0.1M BIS-TRIS PH8.0, 22% PEG3350 (W/V) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 20, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→57.44 Å / Num. obs: 41858 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 36.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 4 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.6 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CHO Resolution: 2.2→90.92 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.923 / SU B: 10.841 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS
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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: 39.689 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→90.92 Å
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Refine LS restraints |
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