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Yorodumi- PDB-5gz8: Crystal structure of catalytic domain of Protein O-mannosyl Kinas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gz8 | |||||||||
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Title | Crystal structure of catalytic domain of Protein O-mannosyl Kinase in ligand-free form | |||||||||
Components | Protein O-mannose kinase | |||||||||
Keywords | TRANSFERASE / Sugar Kinase / Dystroglycanopathy / O-mannosylation | |||||||||
Function / homology | Function and homology information glycoprotein-mannosyl O6-kinase / O-linked glycosylation / carbohydrate kinase activity / phosphotransferase activity, alcohol group as acceptor / carbohydrate phosphorylation / protein O-linked glycosylation / neuromuscular process / sensory perception of pain / brain development / learning or memory ...glycoprotein-mannosyl O6-kinase / O-linked glycosylation / carbohydrate kinase activity / phosphotransferase activity, alcohol group as acceptor / carbohydrate phosphorylation / protein O-linked glycosylation / neuromuscular process / sensory perception of pain / brain development / learning or memory / protein kinase activity / protein phosphorylation / endoplasmic reticulum membrane / ATP binding Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | |||||||||
Authors | Nagae, M. / Yamaguchi, Y. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Genes Cells / Year: 2017 Title: 3D structural analysis of protein O-mannosyl kinase, POMK, a causative gene product of dystroglycanopathy. Authors: Nagae, M. / Mishra, S.K. / Neyazaki, M. / Oi, R. / Ikeda, A. / Matsugaki, N. / Akashi, S. / Manya, H. / Mizuno, M. / Yagi, H. / Kato, K. / Senda, T. / Endo, T. / Nogi, T. / Yamaguchi, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gz8.cif.gz | 65.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gz8.ent.gz | 50.1 KB | Display | PDB format |
PDBx/mmJSON format | 5gz8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/5gz8 ftp://data.pdbj.org/pub/pdb/validation_reports/gz/5gz8 | 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: 35213.105 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 45-349 / Mutation: N66Q, N164Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pomk, Sgk196 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) References: UniProt: Q3TUA9, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
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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: 4.06 Å3/Da / Density % sol: 69.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Tris-HCl (pH 8.5), 23%(w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 25, 2016 |
Radiation | Monochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→100 Å / Num. obs: 200696 / % possible obs: 99.8 % / Redundancy: 9.8 % / Rsym value: 0.102 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.631 / Mean I/σ(I) obs: 2.9 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→39.456 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.81
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→39.456 Å
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Refine LS restraints |
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LS refinement shell |
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