+Open data
-Basic information
Entry | Database: PDB / ID: 2xsa | ||||||
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Title | OgOGA apostructure | ||||||
Components | HYALURONOGLUCOSAMINIDASEHyaluronidase | ||||||
Keywords | HYDROLASE / O-GLCNACYLATION / O-GLCNACASE / GLYCOSYL HYDROLASE | ||||||
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 Similarity search - Function | ||||||
Biological species | OCEANICOLA GRANULOSUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Schuttelkopf, A.W. / van Aalten, D.M.F. | ||||||
Citation | Journal: Biochem.J. / Year: 2010 Title: Human Oga Binds Substrates in a Conserved Peptide Recognition Groove. Authors: Schimpl, M. / Schuttelkopf, A.W. / Borodkin, V.S. / Van Aalten, D.M.F. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" 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 | 2xsa.cif.gz | 191.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xsa.ent.gz | 159.4 KB | Display | PDB format |
PDBx/mmJSON format | 2xsa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xs/2xsa ftp://data.pdbj.org/pub/pdb/validation_reports/xs/2xsa | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 50098.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) OCEANICOLA GRANULOSUS (bacteria) / Strain: HTCC2516 / Plasmid: PGEX-6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2CEE3, beta-N-acetylhexosaminidase |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 48 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 18% POLYETHYLENE GLYCOL 4000, 100-250 MM MGCL2, 100 MM TRIS/HCL, PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 |
Detector | Type: MARRESEARCH / Detector: CCD / Details: MIRRORS |
Radiation | Monochromator: SI MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. obs: 31362 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 36.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 33.8 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 5.6 / % possible all: 94.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 9.352 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.53 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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