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Yorodumi- PDB-1ypu: Human Oxidized Low Density Lipoprotein Receptor LOX-1 C2 Space Group -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ypu | ||||||
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Title | Human Oxidized Low Density Lipoprotein Receptor LOX-1 C2 Space Group | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.05 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 | 1ypu.cif.gz | 70.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ypu.ent.gz | 52 KB | Display | PDB format |
PDBx/mmJSON format | 1ypu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/1ypu ftp://data.pdbj.org/pub/pdb/validation_reports/yp/1ypu | HTTPS FTP |
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-Related structure data
Related structure data | 1ypoC 1ypqC 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: 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: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 11, 2004 / Details: OSMIC MIRROR |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 16573 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 8.8 Å2 / Rsym value: 0.034 / Net I/σ(I): 29 |
Reflection shell | Resolution: 2.05→2.12 Å / Mean I/σ(I) obs: 12 / Rsym value: 0.082 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MPU, 1K9I, 1Q03 Resolution: 2.05→10 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 391891.53 / 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: 57.0277 Å2 / ksol: 0.469489 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.18 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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