+Open data
-Basic information
Entry | Database: PDB / ID: 5m7r | |||||||||
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Title | Structure of human O-GlcNAc hydrolase | |||||||||
Components | Protein O-GlcNAcase | |||||||||
Keywords | HYDROLASE / human glacoside hydrolase GlcNAc | |||||||||
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: 2.35 Å | |||||||||
Authors | Roth, C. / Chan, S. / Offen, W.A. / Hemsworth, G.R. / Willems, L.I. / King, D. / Varghese, V. / Britton, R. / Vocadlo, D.J. / Davies, G.J. | |||||||||
Funding support | United Kingdom, Canada, 2items
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Citation | Journal: Nat. Chem. Biol. / Year: 2017 Title: Structural and functional insight into human O-GlcNAcase. Authors: Roth, C. / Chan, S. / Offen, W.A. / Hemsworth, G.R. / Willems, L.I. / King, D.T. / Varghese, V. / Britton, R. / Vocadlo, D.J. / Davies, G.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m7r.cif.gz | 311.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m7r.ent.gz | 245.5 KB | Display | PDB format |
PDBx/mmJSON format | 5m7r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5m7r_validation.pdf.gz | 448.7 KB | Display | wwPDB validaton report |
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Full document | 5m7r_full_validation.pdf.gz | 458.4 KB | Display | |
Data in XML | 5m7r_validation.xml.gz | 32.4 KB | Display | |
Data in CIF | 5m7r_validation.cif.gz | 45 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m7/5m7r ftp://data.pdbj.org/pub/pdb/validation_reports/m7/5m7r | HTTPS FTP |
-Related structure data
Related structure data | 5m7sC 5m7tC 5m7uC 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: 103020.906 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: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Gold 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: 2.5 Å3/Da / Density % sol: 50.7 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion Details: 0.14 - 0.2 M triammonium citrate pH 7.5, 16-20 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→96.25 Å / Num. obs: 641548 / % possible obs: 100 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.033 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.35→2.41 Å / Redundancy: 10 % / Rmerge(I) obs: 2.186 / Mean I/σ(I) obs: 1 / Num. measured obs: 4442 / CC1/2: 0.628 / Rpim(I) all: 0.703 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2cho Resolution: 2.35→96.25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.254 / ESU R Free: 0.208 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 176.69 Å2 / Biso mean: 80.962 Å2 / Biso min: 38.42 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→96.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.411 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 1.034 Å / Origin y: 1.827 Å / Origin z: 32.46 Å
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