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Yorodumi- PDB-1ypq: Human Oxidized Low Density Lipoprotein Receptor LOX-1 Dioxane Complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ypq | ||||||
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Title | Human Oxidized Low Density Lipoprotein Receptor LOX-1 Dioxane Complex | ||||||
Components | oxidised low density lipoprotein (lectin-like) receptor 1 | ||||||
Keywords | IMMUNE SYSTEM / Oxidized low density Lipoprotein receptor / Lox-1 / CTLD / C-type lectin like domain / NK Cell receptor | ||||||
Function / homology | Function and homology information low-density lipoprotein particle receptor activity / lipoprotein metabolic process / blood circulation / leukocyte cell-cell adhesion / immune system process / tertiary granule membrane / specific granule membrane / Cell surface interactions at the vascular wall / carbohydrate binding / receptor complex ...low-density lipoprotein particle receptor activity / lipoprotein metabolic process / blood circulation / leukocyte cell-cell adhesion / immune system process / tertiary granule membrane / specific granule membrane / Cell surface interactions at the vascular wall / carbohydrate binding / receptor complex / inflammatory response / membrane raft / intracellular membrane-bounded organelle / Neutrophil degranulation / proteolysis / extracellular region / nucleoplasm / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Park, H. / Adsit, F.G. / Boyington, J.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: The 1.4 angstrom crystal structure of the human oxidized low density lipoprotein receptor lox-1. Authors: Park, H. / Adsit, F.G. / Boyington, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ypq.cif.gz | 75.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ypq.ent.gz | 54.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ypq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/1ypq ftp://data.pdbj.org/pub/pdb/validation_reports/yp/1ypq | HTTPS FTP |
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-Related structure data
Related structure data | 1ypoC 1ypuC 1k9iS 1mpuS 1q03S C: citing same article (ref.) 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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Unit cell |
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Components on special symmetry positions |
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Details | biological assembly is dimer, the two asymmetric molecules |
-Components
#1: Protein | Mass: 15312.383 Da / Num. of mol.: 2 / Fragment: C-Type Lectin-Like Domain (Residues 136-273) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P78380 #2: Chemical | ChemComp-DIO / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal |
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Crystal grow |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 12, 2004 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 50675 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 14.9 Å2 / Rsym value: 0.053 / Net I/σ(I): 25 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.31 / % possible all: 91.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MPU, 1K9I, 1Q03 Resolution: 1.4→9.96 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 499658.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 66.7117 Å2 / ksol: 0.458554 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.4→9.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.49 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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