+Open data
-Basic information
Entry | Database: PDB / ID: 1k8i | ||||||
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Title | CRYSTAL STRUCTURE OF MOUSE H2-DM | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC | ||||||
Function / homology | Function and homology information positive regulation of humoral immune response / positive regulation of germinal center formation / MHC class II antigen presentation / positive thymic T cell selection / positive regulation of T cell differentiation / antigen processing and presentation / inner ear development / chaperone cofactor-dependent protein refolding / immunoglobulin mediated immune response / multivesicular body ...positive regulation of humoral immune response / positive regulation of germinal center formation / MHC class II antigen presentation / positive thymic T cell selection / positive regulation of T cell differentiation / antigen processing and presentation / inner ear development / chaperone cofactor-dependent protein refolding / immunoglobulin mediated immune response / multivesicular body / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / protein transport / late endosome / MHC class II protein complex binding / late endosome membrane / protein-containing complex assembly / adaptive immune response / membrane => GO:0016020 / lysosome / endosome membrane / lysosomal membrane / intracellular membrane-bounded organelle / cell surface Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / molecular replacement,MIR / Resolution: 3.1 Å | ||||||
Authors | Fremont, D.H. / Crawford, F. / Marrack, P. / Hendrickson, W. / Kappler, J. | ||||||
Citation | Journal: Immunity / Year: 1998 Title: Crystal structure of mouse H2-M. Authors: Fremont, D.H. / Crawford, F. / Marrack, P. / Hendrickson, W.A. / Kappler, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k8i.cif.gz | 81.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k8i.ent.gz | 65.1 KB | Display | PDB format |
PDBx/mmJSON format | 1k8i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k8i_validation.pdf.gz | 395.9 KB | Display | wwPDB validaton report |
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Full document | 1k8i_full_validation.pdf.gz | 407.1 KB | Display | |
Data in XML | 1k8i_validation.xml.gz | 10 KB | Display | |
Data in CIF | 1k8i_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/1k8i ftp://data.pdbj.org/pub/pdb/validation_reports/k8/1k8i | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21466.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-DM / Cell line (production host): high-five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P28078 |
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#2: Protein | Mass: 21329.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-DM / Cell line (production host): high-five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q31099 |
#3: Sugar |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 4.57 Å3/Da / Density % sol: 73.09 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M lithium sulfate, 0.1M MES, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Details: used microseeding | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 1, 1998 / Details: mirrors |
Radiation | Monochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→20 Å / Num. all: 13888 / Num. obs: 13711 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 4.56 % / Biso Wilson estimate: 74.5 Å2 / Rsym value: 0.091 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 3.1→3.2 Å / Mean I/σ(I) obs: 1.71 / Num. unique all: 1303 / Rsym value: 0.482 / % possible all: 95.2 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 13888 / Num. measured all: 63314 / Rmerge(I) obs: 0.091 |
Reflection shell | *PLUS % possible obs: 95.2 % / Rmerge(I) obs: 0.482 |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement,MIR / Resolution: 3.1→12 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 64.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.1→12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.21 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Highest resolution: 3.1 Å / Lowest resolution: 12 Å / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 3.1 Å / Lowest resolution: 3.2 Å / Rfactor Rfree: 0.334 / Rfactor Rwork: 0.345 / Num. reflection obs: 1303 / Rfactor obs: 0.345 |