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Yorodumi- PDB-4ixd: X-ray structure of lfa-1 i-domain in complex with ibe-667 at 1.8a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ixd | ||||||
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Title | X-ray structure of lfa-1 i-domain in complex with ibe-667 at 1.8a resolution | ||||||
Components | Integrin alpha-L | ||||||
Keywords | IMMUNE SYSTEM / ROSSMAN-FOLD / I-DOMAIN | ||||||
Function / homology | Function and homology information memory T cell extravasation / integrin alphaL-beta2 complex / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / ICAM-3 receptor activity / RUNX3 Regulates Immune Response and Cell Migration / integrin complex / cell adhesion mediated by integrin / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / receptor clustering ...memory T cell extravasation / integrin alphaL-beta2 complex / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / ICAM-3 receptor activity / RUNX3 Regulates Immune Response and Cell Migration / integrin complex / cell adhesion mediated by integrin / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / receptor clustering / Integrin cell surface interactions / specific granule membrane / phagocytosis / cell adhesion molecule binding / cell-matrix adhesion / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / cell-cell adhesion / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / cell adhesion / inflammatory response / external side of plasma membrane / Neutrophil degranulation / cell surface / signal transduction / extracellular exosome / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Kallen, J. | ||||||
Citation | Journal: To be Published / Year: 2013 Title: Identification and x-ray structure based investigation of an ICAM-1 binding enhancing small molecule activator of LFA-1 Authors: Hintersteiner, M. / Kallen, J. / Schmied, M. / Jung, T. / Graf, C. / Mudd, G. / Gstach, H. / Auer, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ixd.cif.gz | 60 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ixd.ent.gz | 42.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ixd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/4ixd ftp://data.pdbj.org/pub/pdb/validation_reports/ix/4ixd | HTTPS FTP |
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-Related structure data
Related structure data | 1xdgS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 21425.561 Da / Num. of mol.: 1 / Fragment: I-DOMAIN, UNP residues 152-336 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAL, CD11A / Plasmid: PET17B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 PLYSS / References: UniProt: P20701 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-1HV / |
#4: Water | ChemComp-HOH / |
Sequence details | THE RESIDUE 189 IS TRP ACCORDING TO LARSON R.S. ET AL. [J. CELL BIOL. 108:703-712(1989)] OR LOFTUS ...THE RESIDUE 189 IS TRP ACCORDING TO LARSON R.S. ET AL. [J. CELL BIOL. 108:703-712(1989)] OR LOFTUS B.J. ET AL.[GENOMICS 60:295-308(1999)] |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 4.6 Details: 0.085M sodium acetate, pH4.6, 0.17M ammonium acetate, 15% glycerol and 25.5% (w/v) PEG4000 , VAPOR DIFFUSION, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.873 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 28, 2000 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→8 Å / Num. all: 18740 / Num. obs: 18688 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.134 / Mean I/σ(I) obs: 10.6 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1XDG Resolution: 1.8→7.97 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 1.996 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.118 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.01 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→7.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.844 Å / Total num. of bins used: 20
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