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Open data
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Basic information
Entry | Database: PDB / ID: 7skg | ||||||
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Title | Myocilin OLF mutant V329M | ||||||
![]() | Myocilin, C-terminal fragment![]() | ||||||
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Function / homology | ![]() skeletal muscle hypertrophy / clustering of voltage-gated sodium channels / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 92.4 KB | Display | ![]() |
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PDB format | ![]() | 53.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7sibC ![]() 7sijC ![]() 7sjtC ![]() 7sjuC ![]() 7sjvC ![]() 7sjwC ![]() 7skdC ![]() 7skeC ![]() 7skfC ![]() 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: 31229.047 Da / Num. of mol.: 1 / Fragment: Olfactomedin Domain / Mutation: V329M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() | ||||||||
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#2: Chemical | ![]() #3: Chemical | ChemComp-CA / | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.2 % |
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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: Jul 28, 2021 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.33→35.69 Å / Num. obs: 56446 / % possible obs: 98.7 % / Redundancy: 5.8 % / Biso Wilson estimate: 9.64 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.08655 / Rpim(I) all: 0.03877 / Rrim(I) all: 0.09507 / Net I/σ(I): 23.02 |
Reflection shell | Resolution: 1.33→1.378 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.5007 / Mean I/σ(I) obs: 5.58 / Num. unique obs: 5575 / CC1/2: 0.892 / CC star: 0.971 / Rpim(I) all: 0.2337 / Rrim(I) all: 0.5543 / % possible all: 98.03 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6pke Resolution: 1.33→35.69 Å / SU ML: 0.1292 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.2212 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: 13.43 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.33→35.69 Å
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Refine LS restraints |
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LS refinement shell |
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