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Yorodumi- PDB-5uhk: Crystal structure of the core catalytic domain of Human O-GlcNAcase -
+Open data
-Basic information
Entry | Database: PDB / ID: 5uhk | ||||||
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Title | Crystal structure of the core catalytic domain of Human O-GlcNAcase | ||||||
Components |
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Keywords | HYDROLASE / O-GLCNACASE / GH84 / ENZYME | ||||||
Function / homology | Function and homology information glycoprotein metabolic process / hyalurononglucosaminidase activity / 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 O-linked glycosylation / protein deglycosylation ...glycoprotein metabolic process / hyalurononglucosaminidase activity / 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 O-linked glycosylation / protein deglycosylation / beta-N-acetylglucosaminidase activity / membrane / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.97 Å | ||||||
Authors | Klein, D.J. / Elsen, N.L. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of the core catalytic domain of human O-GlcNAcase and molecular basis of activity and inhibition Authors: Elsen, N.L. / Patel, S.B. / Ford, R.E. / Hall, D.L. / Hess, F. / Kandula, H. / Kornienko, M. / Lumb, K.J. / Reid, J. / Selnick, H. / Shipman, J.M. / Sharma, S. / Soisson, S.M. / Klein, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5uhk.cif.gz | 184.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uhk.ent.gz | 145.2 KB | Display | PDB format |
PDBx/mmJSON format | 5uhk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uh/5uhk ftp://data.pdbj.org/pub/pdb/validation_reports/uh/5uhk | HTTPS FTP |
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-Related 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: 39987.340 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MGEA5, HEXC, KIAA0679, MEA5 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: O60502, protein O-GlcNAcase, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds #2: Protein | Mass: 18786.576 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MGEA5, HEXC, KIAA0679, MEA5 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: O60502, protein O-GlcNAcase, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds #3: Chemical | #4: 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: 2.56 Å3/Da / Density % sol: 51.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 14-17% PEG 3350, 0.2 M Mg Formate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.97→128 Å / Num. obs: 24942 / % possible obs: 95.9 % / Redundancy: 12.8 % / Biso Wilson estimate: 104.27 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 2.97→2.98 Å / Redundancy: 12.6 % / Rmerge(I) obs: 1.055 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.927 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 2.97→34.24 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.878 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.395
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Displacement parameters | Biso mean: 102.94 Å2
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Refine analyze | Luzzati coordinate error obs: 0.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.97→34.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.97→3.1 Å / Rfactor Rfree error: 0 / Total num. of bins used: 12
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