+Open data
-Basic information
Entry | Database: PDB / ID: 5tke | ||||||
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Title | Crystal Structure of Eukaryotic Hydrolase | ||||||
Components | O-GlcNAcase: chimera construct | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information hyalurononglucosaminidase activity / glycoprotein metabolic process / N-acetylglucosamine metabolic process / glycoprotein catabolic process / protein O-GlcNAcase / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / protein deglycosylation / protein O-linked glycosylation / beta-N-acetylglucosaminidase activity / identical protein binding ...hyalurononglucosaminidase activity / glycoprotein metabolic process / N-acetylglucosamine metabolic process / glycoprotein catabolic process / protein O-GlcNAcase / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / protein deglycosylation / protein O-linked glycosylation / beta-N-acetylglucosaminidase activity / identical protein binding / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.481 Å | ||||||
Authors | Li, B. / Jiang, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat. Struct. Mol. Biol. / Year: 2017 Title: Structures of human O-GlcNAcase and its complexes reveal a new substrate recognition mode. Authors: Li, B. / Li, H. / Lu, L. / Jiang, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tke.cif.gz | 375.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tke.ent.gz | 306.4 KB | Display | PDB format |
PDBx/mmJSON format | 5tke.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tk/5tke ftp://data.pdbj.org/pub/pdb/validation_reports/tk/5tke | HTTPS FTP |
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-Related structure data
Related structure data | 5un8C 5un9C 2cbjS 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: 57823.566 Da / Num. of mol.: 2 / Fragment: unp residues 60-542; unp residues 553-704 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MGEA5, HEXC, KIAA0679, MEA5 Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: O60502, protein O-GlcNAcase, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.71 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 7 Details: 0.032 M ammonium citrate tribasic (pH 7.0), 0.02 M MES monohydrate, 0.016 M imidazole, 0.002 M zinc sulfate heptahydrate, 0.128 M potassium thiocyanate, 12.8% w/v polyethylene glycol 3,350, ...Details: 0.032 M ammonium citrate tribasic (pH 7.0), 0.02 M MES monohydrate, 0.016 M imidazole, 0.002 M zinc sulfate heptahydrate, 0.128 M potassium thiocyanate, 12.8% w/v polyethylene glycol 3,350, 3.2% w/v polyethylene glycol monomethyl ether 2,000, and 5% w/v polyethylene glycol monomethyl ether 550 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.978 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.48→50 Å / Num. obs: 44255 / % possible obs: 100 % / Redundancy: 6.4 % / Net I/σ(I): 19.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2cbj Resolution: 2.481→44.249 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.25 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.481→44.249 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -16.201 Å / Origin y: -63.9248 Å / Origin z: 97.0115 Å
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Refinement TLS group | Selection details: all |