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- PDB-6ibo: Catalytic deficiency of O-GlcNAc transferase leads to X-linked in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ibo | ||||||
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Title | Catalytic deficiency of O-GlcNAc transferase leads to X-linked intellectual disability | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gundogdu, M. / van Aalten, D.M.F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Catalytic deficiency of O-GlcNAc transferase leads to X-linked intellectual disability. Authors: Pravata, V.M. / Muha, V. / Gundogdu, M. / Ferenbach, A.T. / Kakade, P.S. / Vandadi, V. / Wilmes, A.C. / Borodkin, V.S. / Joss, S. / Stavridis, M.P. / van Aalten, D.M.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 165.5 KB | Display | ![]() |
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PDB format | ![]() | 125.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5c1dS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 80989.586 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() | ||
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#2: Protein/peptide | Mass: 932.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: KKVAVSRA / Source: (synth.) ![]() ![]() | ||
#3: Chemical | ChemComp-12V / ( | ||
#4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.14 % / Description: Large and amorphous |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.45 M K2HPO4, 8 mM EDTA and 1% xylitol / Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 80 K / Ambient temp details: under cryostream / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.5→100 Å / Num. obs: 286887 / % possible obs: 100 % / Redundancy: 5.2 % / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.17→2.23 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 23302 / CC1/2: 0.848 / Rsym value: 0.91 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5C1D Resolution: 2.17→100 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 8.002 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.19 / 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: 54.861 Å2
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Refinement step | Cycle: 1 / Resolution: 2.17→100 Å
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Refine LS restraints |
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