+Open data
-Basic information
Entry | Database: PDB / ID: 6r45 | ||||||
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Title | Crystal structure of eukaryotic O-GlcNAcase HAT-like domain | ||||||
Components | O-GlcNAcase | ||||||
Keywords | TRANSFERASE / O-GlcNAcase / Eukaryote / acetyltransferase / Trichoplax adhaerens | ||||||
Function / homology | : / : / protein O-GlcNAcase / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / metabolic process / Glycoside hydrolase superfamily / O-GlcNAcase Function and homology information | ||||||
Biological species | Trichoplax adhaerens (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.784 Å | ||||||
Authors | Raimi, O.G. / Gorelik, A. / Hopkins-Navratilova, I. / Aristotelous, T. / Ferenbach, A. / vanAalten, D. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Crystal structure of eukaryotic O-GlcNAcase HAT-like domain Authors: Raimi, O.G. / Gorelik, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r45.cif.gz | 100.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r45.ent.gz | 75.8 KB | Display | PDB format |
PDBx/mmJSON format | 6r45.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/6r45 ftp://data.pdbj.org/pub/pdb/validation_reports/r4/6r45 | HTTPS FTP |
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-Related structure data
Related structure data | 4bmhS S: Starting model for refinement |
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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: 24833.211 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trichoplax adhaerens (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D5X2Y8, protein O-GlcNAcase #2: Chemical | ChemComp-TRS / | #3: 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: 2.26 Å3/Da / Density % sol: 45.48 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.1 M HEPES 7.5, 60 mM Sodium potassium-tartrate and 27.5 % PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.965 Å / Relative weight: 1 |
Reflection | Resolution: 1.784→59.59 Å / Num. obs: 36731 / % possible obs: 89 % / Redundancy: 1.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.07 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.784→1.848 Å / Num. unique obs: 3663 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4BMH Resolution: 1.784→36.36 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.146 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.141 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.125 Å2
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Refinement step | Cycle: 1 / Resolution: 1.784→36.36 Å
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Refine LS restraints |
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