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Open data
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Basic information
Entry | Database: PDB / ID: 7nmy | ||||||
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Title | Crystal structure of beta-2-microglobulin D76Y mutant | ||||||
![]() | Beta-2-microglobulin![]() | ||||||
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Function / homology | ![]() positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion ...positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Guthertz, N. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The effect of mutation on an aggregation-prone protein: An in vivo, in vitro, and in silico analysis. Authors: Guthertz, N. / van der Kant, R. / Martinez, R.M. / Xu, Y. / Trinh, C. / Iorga, B.I. / Rousseau, F. / Schymkowitz, J. / Brockwell, D.J. / Radford, S.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7nmcC ![]() 7nmoC ![]() 7nmrC ![]() 7nmtC ![]() 7nmvC ![]() 7nn5C ![]() 2yxfS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | ![]() Mass: 11927.443 Da / Num. of mol.: 1 / Mutation: D76Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.23 % / Description: One molecule per asymmetric unit |
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Crystal grow![]() | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 100 nL mother liquor / 200 nL protein 15% Glycerol, 0.1 M NaAcetate pH 4.5-5.5, 28-32%PEG 4000, 0.2 M NH4Acetate PH range: 4.5 - 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.25→43.98 Å / Num. obs: 24565 / % possible obs: 98 % / Redundancy: 7 % / CC1/2: 0.999 / Rpim(I) all: 0.032 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.25→1.27 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 988 / CC1/2: 0.448 / Rpim(I) all: 0.927 / % possible all: 81.4 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2YXF Resolution: 1.25→43.98 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.744 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.059 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.957 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→43.98 Å
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Refine LS restraints |
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LS refinement shell |
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