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Yorodumi- PDB-4wxs: Crystal Structure of the E396D SNP Variant of the Myocilin Olfact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wxs | ||||||
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Title | Crystal Structure of the E396D SNP Variant of the Myocilin Olfactomedin Domain | ||||||
Components | Myocilin | ||||||
Keywords | PROTEIN BINDING / beta propeller / 5 bladed propeller / olfactomedin | ||||||
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 / positive regulation of substrate adhesion-dependent cell spreading / rough endoplasmic reticulum / 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 / Resolution: 1.9 Å | ||||||
Authors | Donegan, R.K. / Freeman, D.M. / Lieberman, R.L. | ||||||
Citation | Journal: Hum.Mol.Genet. / Year: 2015 Title: Structural basis for misfolding in myocilin-associated glaucoma. Authors: Donegan, R.K. / Hill, S.E. / Freeman, D.M. / Nguyen, E. / Orwig, S.D. / Turnage, K.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 | 4wxs.cif.gz | 74.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wxs.ent.gz | 57.1 KB | Display | PDB format |
PDBx/mmJSON format | 4wxs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wx/4wxs ftp://data.pdbj.org/pub/pdb/validation_reports/wx/4wxs | 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 31182.957 Da / Num. of mol.: 1 / Mutation: E396D 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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-Non-polymers , 6 types, 311 molecules
#2: Chemical | ChemComp-CA / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-PG4 / | #5: Chemical | ChemComp-P6G / | #6: Chemical | ChemComp-NA / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.2 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: Peg 3000 CAPSO Peg 400 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 23, 2013 / Details: Mar CCD 300 - not listed as an option |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→19.79 Å / Num. obs: 130265 / % possible obs: 99.98 % / Redundancy: 6.2 % / Net I/σ(I): 15.52 |
-Processing
Software |
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Refinement | Resolution: 1.9→19.79 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.2 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→19.79 Å
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Refine LS restraints |
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LS refinement shell |
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