+Open data
-Basic information
Entry | Database: PDB / ID: 6xsd | ||||||
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Title | Patient-derived B2GPI | ||||||
Components | Beta-2-glycoprotein 1 | ||||||
Keywords | BLOOD CLOTTING / Plasma protein / antibody binding / antiphospholipid syndrome | ||||||
Function / homology | Function and homology information lipoprotein lipase activator activity / triglyceride transport / platelet dense granule lumen / negative regulation of complement activation, classical pathway / T cell mediated immunity / positive regulation of lipoprotein lipase activity / blood coagulation, intrinsic pathway / chylomicron / negative regulation of myeloid cell apoptotic process / regulation of fibrinolysis ...lipoprotein lipase activator activity / triglyceride transport / platelet dense granule lumen / negative regulation of complement activation, classical pathway / T cell mediated immunity / positive regulation of lipoprotein lipase activity / blood coagulation, intrinsic pathway / chylomicron / negative regulation of myeloid cell apoptotic process / regulation of fibrinolysis / very-low-density lipoprotein particle / negative regulation of blood coagulation / high-density lipoprotein particle / negative regulation of endothelial cell migration / triglyceride metabolic process / plasminogen activation / negative regulation of endothelial cell proliferation / negative regulation of smooth muscle cell apoptotic process / positive regulation of blood coagulation / negative regulation of fibrinolysis / negative regulation of angiogenesis / phospholipid binding / Platelet degranulation / heparin binding / collagen-containing extracellular matrix / lipid binding / cell surface / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å | ||||||
Authors | Klenotic, P.A. / Yu, E.W.Y. | ||||||
Citation | Journal: To Be Published Title: B2-Glycoprotein I and it's role in APS Authors: Klenotic, P.A. / Yu, E.W.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xsd.cif.gz | 143.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xsd.ent.gz | 112.4 KB | Display | PDB format |
PDBx/mmJSON format | 6xsd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xs/6xsd ftp://data.pdbj.org/pub/pdb/validation_reports/xs/6xsd | HTTPS FTP |
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-Related structure data
Related structure data | 1qubS 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
#1: Protein | Mass: 36299.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02749 | ||||
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#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 100mM Hepes, pH 7.5, 1.8M Ammonium Sulfate |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.54→50 Å / Num. obs: 50299 / % possible obs: 99.9 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.214 / Rpim(I) all: 0.075 / Rrim(I) all: 0.227 / Χ2: 1 / Net I/σ(I): 6.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1qub Resolution: 2.54→47.86 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.2 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 186.47 Å2 / Biso mean: 79.1212 Å2 / Biso min: 44.21 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.54→47.86 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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