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Yorodumi- PDB-6ou3: Crystal Structure of the D478S Variant of the Myocilin Olfactomed... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ou3 | ||||||
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Title | Crystal Structure of the D478S Variant of the Myocilin Olfactomedin Domain | ||||||
Components | Myocilin | ||||||
Keywords | PROTEIN BINDING / olfactomedin myocilin beta propeller | ||||||
Function / homology | Function and homology information skeletal muscle hypertrophy / clustering of voltage-gated sodium channels / myosin light chain binding / non-canonical Wnt signaling pathway / myelination in peripheral nervous system / node of Ranvier / frizzled binding / negative regulation of stress fiber assembly / negative regulation of Rho protein signal transduction / positive regulation of mitochondrial depolarization ...skeletal muscle hypertrophy / clustering of voltage-gated sodium channels / myosin light chain binding / non-canonical Wnt signaling pathway / myelination in peripheral nervous system / node of Ranvier / frizzled binding / negative regulation of stress fiber assembly / negative regulation of Rho protein signal transduction / positive regulation of mitochondrial depolarization / negative regulation of cell-matrix adhesion / ERBB2-ERBB3 signaling pathway / positive regulation of focal adhesion assembly / regulation of MAPK cascade / fibronectin binding / rough endoplasmic reticulum / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / positive regulation of JNK cascade / bone development / mitochondrial intermembrane space / cilium / receptor tyrosine kinase binding / osteoblast differentiation / neuron projection development / cytoplasmic vesicle / collagen-containing extracellular matrix / mitochondrial outer membrane / mitochondrial inner membrane / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / Golgi apparatus / endoplasmic reticulum / signal transduction / extracellular space / extracellular exosome / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.796 Å | ||||||
Authors | Hill, S.E. / Kwon, M.S. / Lieberman, R.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Stable calcium-free myocilin olfactomedin domain variants reveal challenges in differentiating between benign and glaucoma-causing mutations. Authors: Hill, S.E. / Kwon, M.S. / Martin, M.D. / Suntharalingam, A. / Hazel, A. / Dickey, C.A. / Gumbart, J.C. / Lieberman, R.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ou3.cif.gz | 107.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ou3.ent.gz | 86.1 KB | Display | PDB format |
PDBx/mmJSON format | 6ou3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/6ou3 ftp://data.pdbj.org/pub/pdb/validation_reports/ou/6ou3 | 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: 31168.973 Da / Num. of mol.: 1 / Fragment: Olfactomedin domain / Mutation: D478S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MYOC, GLC1A, TIGR / Production host: Escherichia coli (E. coli) / References: UniProt: Q99972 | ||
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#2: Chemical | ChemComp-NA / | ||
#3: Chemical | #4: 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: 1.88 Å3/Da / Density % sol: 34.71 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 3350, 0.2 M Bis Tris pH 6.0, 0.4 M Magnesium formate |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 26, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.796→40.544 Å / Num. obs: 22530 / % possible obs: 99.56 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.1266 / Net I/σ(I): 15.02 |
Reflection shell | Resolution: 1.796→1.86 Å / Mean I/σ(I) obs: 2.9 / Num. unique obs: 2139 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.796→40.544 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 15.68
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.796→40.544 Å
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Refine LS restraints |
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LS refinement shell |
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