+Open data
-Basic information
Entry | Database: PDB / ID: 5abh | ||||||
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Title | Structure of GH84 with ligand | ||||||
Components | O-GLCNACASE BT_4395 | ||||||
Keywords | HYDROLASE / TIM-BARREL / INHIBITOR | ||||||
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 / OTHER / Resolution: 1.95 Å | ||||||
Authors | Bergeron-Brlek, M. / Goodwin-Tindall, J. / Cekic, N. / Varghese, V. / Zandberg, W.F. / Shan, X. / Roth, C. / Chan, S. / Davies, G.J. / Vocadlo, D.J. / Britton, R. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2015 Title: A Convenient Approach to Stereoisomeric Iminocyclitols: Generation of Potent Brain-Permeable Oga Inhibitors. Authors: Bergeron-Brlek, M. / Goodwin-Tindall, J. / Cekic, N. / Roth, C. / Zandberg, W.F. / Shan, X. / Varghese, V. / Chan, S. / Davies, G.J. / Vocadlo, D.J. / Britton, R. | ||||||
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. SHEET DETERMINATION METHOD: DSSP 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5abh.cif.gz | 559.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5abh.ent.gz | 478.4 KB | Display | PDB format |
PDBx/mmJSON format | 5abh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/5abh ftp://data.pdbj.org/pub/pdb/validation_reports/ab/5abh | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 83507.398 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 22-737 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): GOLD References: UniProt: Q89ZI2, protein O-GlcNAcase, beta-N-acetylhexosaminidase |
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-Non-polymers , 5 types, 664 molecules
#2: Chemical | ChemComp-CL / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CA / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 57.2 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→129.8 Å / Num. obs: 136504 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 8.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 1.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.95→130.74 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 13.589 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.15 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.257 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→130.74 Å
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Refine LS restraints |
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