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Yorodumi- PDB-5gz9: Crystal structure of catalytic domain of Protein O-mannosyl Kinas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gz9 | |||||||||
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Title | Crystal structure of catalytic domain of Protein O-mannosyl Kinase in complexes with AMP-PNP, Magnesium ions and glycopeptide | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.4 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 | 5gz9.cif.gz | 75.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gz9.ent.gz | 52.8 KB | Display | PDB format |
PDBx/mmJSON format | 5gz9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gz9_validation.pdf.gz | 784.2 KB | Display | wwPDB validaton report |
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Full document | 5gz9_full_validation.pdf.gz | 786.6 KB | Display | |
Data in XML | 5gz9_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 5gz9_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/5gz9 ftp://data.pdbj.org/pub/pdb/validation_reports/gz/5gz9 | HTTPS FTP |
-Related structure data
Related structure data | 5gz8SC 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: 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: Chemical | ChemComp-ANP / | ||||
#3: Chemical | #4: Sugar | ChemComp-MAN / | #5: 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: 3.98 Å3/Da / Density % sol: 69.1 % |
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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: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→100 Å / Num. obs: 249333 / % possible obs: 100 % / Redundancy: 11 % / Rsym value: 0.152 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 11 % / Rmerge(I) obs: 0.742 / Mean I/σ(I) obs: 3.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GZ8 Resolution: 2.4→40.192 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.24
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→40.192 Å
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Refine LS restraints |
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LS refinement shell |
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