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Open data
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Basic information
Entry | Database: PDB / ID: 7skd | ||||||
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Title | Myocilin OLF mutant S331L | ||||||
![]() | Myocilin, C-terminal fragment | ||||||
![]() | CELL ADHESION / olfactomedin / beta-propeller | ||||||
Function / homology | ![]() 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 / receptor tyrosine kinase binding / cilium / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Scelsi, H.S. / Barlow, B.M. / Lieberman, R.L. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.5 KB | Display | ![]() |
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PDB format | ![]() | 49 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.5 KB | Display | ![]() |
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Full document | ![]() | 429.5 KB | Display | |
Data in XML | ![]() | 12.1 KB | Display | |
Data in CIF | ![]() | 16.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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 ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() |
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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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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