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Open data
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Basic information
Entry | Database: PDB / ID: 3ib4 | ||||||
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Title | The double mutant of Beta-2 microglobulin K58P-W60G | ||||||
![]() | 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 | ![]() ![]() ![]() | ||||||
![]() | Colombo, M. / Ricagno, S. / Bolognesi, M. | ||||||
![]() | ![]() Title: Crystal structure of the Beta-2 microglobulin mutant K58P-W60G Authors: Colombo, M. / Ricagno, S. / Bolognesi, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65 KB | Display | ![]() |
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PDB format | ![]() | 47.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2z9tS S: Starting model for refinement |
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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
#1: Protein | ![]() Mass: 11734.133 Da / Num. of mol.: 1 / Mutation: K58P, W60G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-PE4 / ![]() |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.56 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1M NaAcetate, 0.2M CH3COONH4, 20% Glycerol, 22% PEG 4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 26, 2009 / Details: Sagitally focusing Ge(220) and a multilayer |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.25→19.04 Å / Num. obs: 26776 / % possible obs: 99.6 % / Redundancy: 10 % / Biso Wilson estimate: 8.213 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.25→1.32 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 3.2 / Num. unique all: 3812 / % possible all: 97.2 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2z9t Resolution: 1.25→15 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.387 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.92 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.25→1.282 Å / Total num. of bins used: 20
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