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Yorodumi- PDB-5ggg: Crystal structure of human protein O-mannose beta-1,2-N-acetylglu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ggg | ||||||
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Title | Crystal structure of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase form I | ||||||
Components | Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 | ||||||
Keywords | TRANSFERASE / SUGAR BINDING PROTEIN / glycosyltransferase / O-mannosylation / alpha-dystroglycan | ||||||
Function / homology | Function and homology information beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity / Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3 / O-linked glycosylation / localization of cell / reactive gliosis / protein O-linked mannosylation / O-glycan processing / acetylglucosaminyltransferase activity / basement membrane organization / dentate gyrus development ...beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity / Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3 / O-linked glycosylation / localization of cell / reactive gliosis / protein O-linked mannosylation / O-glycan processing / acetylglucosaminyltransferase activity / basement membrane organization / dentate gyrus development / protein O-linked glycosylation / Transferases; Glycosyltransferases; Hexosyltransferases / myelination / sensory perception of sound / gene expression / manganese ion binding / carbohydrate binding / Golgi membrane / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å | ||||||
Authors | Kuwabara, N. / Senda, T. / Kato, R. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Carbohydrate-binding domain of the POMGnT1 stem region modulates O-mannosylation sites of alpha-dystroglycan Authors: Kuwabara, N. / Manya, H. / Yamada, T. / Tateno, H. / Kanagawa, M. / Kobayashi, K. / Akasaka-Manya, K. / Hirose, Y. / Mizuno, M. / Ikeguchi, M. / Toda, T. / Hirabayashi, J. / Senda, T. / Endo, T. / Kato, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ggg.cif.gz | 227.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ggg.ent.gz | 189.3 KB | Display | PDB format |
PDBx/mmJSON format | 5ggg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/5ggg ftp://data.pdbj.org/pub/pdb/validation_reports/gg/5ggg | HTTPS FTP |
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-Related structure data
Related structure data | 5ggfC 5ggiC 5ggjC 5ggkC 5gglC 5ggnC 5ggoC 5ggpC 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: 65551.453 Da / Num. of mol.: 1 / Fragment: UNP residues 92-660 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POMGNT1, MGAT1.2, UNQ746/PRO1475 / Cell line (production host): HEK-293T / Production host: Homo sapiens (human) References: UniProt: Q8WZA1, Transferases; Glycosyltransferases; Hexosyltransferases |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.49 Å3/Da / Density % sol: 72.64 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Na malonate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 31, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→44.684 Å / Num. obs: 45699 / % possible obs: 99.9 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 30.8 |
Reflection shell | Resolution: 3→3.18 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 4.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3→44.684 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.21 Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→44.684 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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