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Open data
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Basic information
Entry | Database: PDB / ID: 1i3r | |||||||||
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Title | CRYSTAL STRUCTURE OF A MUTANT IEK CLASS II MHC MOLECULE | |||||||||
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![]() | IMMUNE SYSTEM / MHC ClassII | |||||||||
Function / homology | ![]() hemoglobin beta binding / positive regulation of myeloid cell differentiation / myeloid cell differentiation / nitric oxide transport / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport ...hemoglobin beta binding / positive regulation of myeloid cell differentiation / myeloid cell differentiation / nitric oxide transport / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport / erythrocyte development / hydrogen peroxide catabolic process / oxygen carrier activity / carbon dioxide transport / regulation of erythrocyte differentiation / oxygen binding / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peroxidase activity / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / adaptive immune response / blood microparticle / lysosomal membrane / heme binding / protein-containing complex binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kappler, J.W. / Wilson, N. | |||||||||
![]() | ![]() Title: Mutations changing the kinetics of class II MHC peptide exchange. Authors: Wilson, N. / Fremont, D. / Marrack, P. / Kappler, J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 331.2 KB | Display | ![]() |
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PDB format | ![]() | 278.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 680.4 KB | Display | ![]() |
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Full document | ![]() | 707.5 KB | Display | |
Data in XML | ![]() | 35.3 KB | Display | |
Data in CIF | ![]() | 55.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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7 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22359.082 Da / Num. of mol.: 4 / Mutation: E11Q, D66N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 25892.832 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.09 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 12.8% PEG4000, 80mM MgCl2, 80mM HEPES pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→25 Å / Num. all: 76526 / Num. obs: 74154 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.445 / % possible all: 90.8 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 25 Å |
Reflection shell | *PLUS % possible obs: 90.8 % / Num. unique obs: 6856 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→25 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 25 Å / σ(F): 0 / Rfactor obs: 0.229 / Rfactor Rfree: 0.27 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 51.9 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.0066 | |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.38 / Num. reflection Rfree: 316 / Rfactor Rwork: 0.331 / Num. reflection obs: 6212 |