+Open data
-Basic information
Entry | Database: PDB / ID: 1i3r | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF A MUTANT IEK CLASS II MHC MOLECULE | |||||||||
Components |
| |||||||||
Keywords | IMMUNE SYSTEM / MHC ClassII | |||||||||
Function / homology | Function and homology information hemoglobin beta binding / positive regulation of myeloid cell differentiation / myeloid cell differentiation / nitric oxide transport / cellular oxidant detoxification / hemoglobin alpha 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 / cellular oxidant detoxification / hemoglobin alpha 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 / 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 / lysosomal membrane / heme binding / protein-containing complex binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Kappler, J.W. / Wilson, N. | |||||||||
Citation | Journal: Immunity / Year: 2001 Title: Mutations changing the kinetics of class II MHC peptide exchange. Authors: Wilson, N. / Fremont, D. / Marrack, P. / Kappler, J. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1i3r.cif.gz | 331.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1i3r.ent.gz | 278.3 KB | Display | PDB format |
PDBx/mmJSON format | 1i3r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1i3r_validation.pdf.gz | 680.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1i3r_full_validation.pdf.gz | 707.5 KB | Display | |
Data in XML | 1i3r_validation.xml.gz | 35.3 KB | Display | |
Data in CIF | 1i3r_validation.cif.gz | 55.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i3/1i3r ftp://data.pdbj.org/pub/pdb/validation_reports/i3/1i3r | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
5 |
| ||||||||
6 |
| ||||||||
7 |
| ||||||||
Unit cell |
|
-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.) Mus musculus (house mouse) / Gene: IEK / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P04224 #2: Protein | Mass: 25892.832 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: IEK / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P02089, GenBank: 199396 #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 / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.09 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 |
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 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→25 Å / Data cutoff high rms absF: 100000 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MLF
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→25 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
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 |