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Open data
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Basic information
Entry | Database: PDB / ID: 7ntp | ||||||
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Title | Human myelin P2 mutant V115A | ||||||
![]() | Myelin P2 protein | ||||||
![]() | LIPID BINDING PROTEIN / myelin / fatty-acid binding protein / Charcot-Marie-Tooth disease | ||||||
Function / homology | ![]() membrane organization / cholesterol binding / fatty acid transport / fatty acid binding / myelin sheath / extracellular exosome / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Uusitalo, M. / Ruskamo, S. / Kursula, P. | ||||||
![]() | ![]() Title: Human myelin protein P2: from crystallography to time-lapse membrane imaging and neuropathy-associated variants. Authors: Uusitalo, M. / Klenow, M.B. / Laulumaa, S. / Blakeley, M.P. / Simonsen, A.C. / Ruskamo, S. / Kursula, P. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 143.2 KB | Display | ![]() |
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PDB format | ![]() | 93.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 358.9 KB | Display | ![]() |
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Full document | ![]() | 362.9 KB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 16.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7nrwC ![]() 7nsrC ![]() 7o60C ![]() 3nr3S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 14963.417 Da / Num. of mol.: 2 / Mutation: V115A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 64.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 2.2 M sodium malonate, pH 7.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033222 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→42.732 Å / Num. obs: 24729 / % possible obs: 99.7 % / Redundancy: 4.93 % / Biso Wilson estimate: 58.98 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.078 / Net I/av σ(I): 11.15 / Net I/σ(I): 11.15 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 5.05 % / Mean I/σ(I) obs: 0.85 / Num. unique obs: 1814 / CC1/2: 0.261 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3NR3 Resolution: 2.1→42.73 Å / SU ML: 0.4103 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.2387 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: 67.73 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→42.73 Å
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Refine LS restraints |
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LS refinement shell |
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