+Open data
-Basic information
Entry | Database: PDB / ID: 7skd | ||||||
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Title | Myocilin OLF mutant S331L | ||||||
Components | Myocilin, C-terminal fragment | ||||||
Keywords | CELL ADHESION / olfactomedin / 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 / negative regulation of cell-matrix adhesion ...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 / negative regulation of cell-matrix adhesion / positive regulation of mitochondrial depolarization / 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 / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / mitochondrial inner membrane / positive regulation of cell migration / Golgi apparatus / signal transduction / endoplasmic reticulum / extracellular space / extracellular exosome / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.712 Å | ||||||
Authors | Scelsi, H.S. / Barlow, B.M. / Lieberman, R.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Dis Model Mech / Year: 2023 Title: Quantitative differentiation of benign and misfolded glaucoma-causing myocilin variants on the basis of protein thermal stability. Authors: Scelsi, H.F. / Hill, K.R. / Barlow, B.M. / Martin, M.D. / 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 | 7skd.cif.gz | 84.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7skd.ent.gz | 49 KB | Display | PDB format |
PDBx/mmJSON format | 7skd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sk/7skd ftp://data.pdbj.org/pub/pdb/validation_reports/sk/7skd | HTTPS FTP |
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-Related structure data
Related structure data | 7sibC 7sijC 7sjtC 7sjuC 7sjvC 7sjwC 7skeC 7skfC 7skgC 7t8dC 6pkeS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31223.062 Da / Num. of mol.: 1 / Fragment: Olfactomedin Domain / Mutation: S331L 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-CA / |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.28 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 10% PEG 8000, 0.05M magnesium chloride |
-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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 20, 2021 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.712→35.13 Å / Num. obs: 21742 / % possible obs: 80.84 % / Redundancy: 6.1 % / Biso Wilson estimate: 18.33 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.09655 / Rpim(I) all: 0.04307 / Rrim(I) all: 0.1062 / Net I/σ(I): 10.58 |
Reflection shell | Resolution: 1.712→1.773 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 2.24 / Num. unique obs: 1000 / CC1/2: 0.934 / CC star: 0.983 / Rpim(I) all: 0.1665 / Rrim(I) all: 0.3573 / % possible all: 37.78 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6pke Resolution: 1.712→35.13 Å / SU ML: 0.2531 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.6324 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.712→35.13 Å
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Refine LS restraints |
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LS refinement shell |
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