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- PDB-6v09: Crystal structure of human recombinant Beta-2 glycoprotein I shor... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6v09 | |||||||||
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Title | Crystal structure of human recombinant Beta-2 glycoprotein I short tag (ST-B2GPI) | |||||||||
![]() | Beta-2-glycoprotein 1 | |||||||||
![]() | BLOOD CLOTTING / PLASMA GLYCOPROTEIN / COAGULATION / INNATE IMMUNE SYSTEM / AUTOIMMUNITY / THROMBOSIS / SUSHI DOMAIN | |||||||||
Function / homology | ![]() lipoprotein lipase activator activity / triglyceride transport / platelet dense granule lumen / positive regulation of lipoprotein lipase activity / negative regulation of complement activation, classical pathway / blood coagulation, intrinsic pathway / T cell mediated immunity / negative regulation of myeloid cell apoptotic process / chylomicron / regulation of fibrinolysis ...lipoprotein lipase activator activity / triglyceride transport / platelet dense granule lumen / positive regulation of lipoprotein lipase activity / negative regulation of complement activation, classical pathway / blood coagulation, intrinsic pathway / T cell mediated immunity / negative regulation of myeloid cell apoptotic process / chylomicron / 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 | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Chen, Z. / Ruben, E.A. / Planer, W. / Chinnaraj, M. / Zuo, X. / Pengo, V. / Macor, P. / Tedesco, F. / Pozzi, N. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The J-elongated conformation of beta2-glycoprotein I predominates in solution: implications for our understanding of antiphospholipid syndrome. Authors: Ruben, E. / Planer, W. / Chinnaraj, M. / Chen, Z. / Zuo, X. / Pengo, V. / De Filippis, V. / Alluri, R.K. / McCrae, K.R. / Macor, P. / Tedesco, F. / Pozzi, N. #1: ![]() Title: CRYSTAL STRUCTURE OF HUMAN BETA2-GLYCOPROTEIN I: IMPLICATIONS FOR PHOSPHOLIPID BINDING AND THE ANTIPHOSPHOLIPID SYNDROME. Authors: Schwarzenbacher, R. / Zeth, K. / Diederichs, K. / Gries, A. / Kostner, G.M. / Laggner, P. / Prassl, R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.7 KB | Display | ![]() |
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PDB format | ![]() | 64.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424 KB | Display | ![]() |
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Full document | ![]() | 424.4 KB | Display | |
Data in XML | ![]() | 2.3 KB | Display | |
Data in CIF | ![]() | 5.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6v06C ![]() 6v08C ![]() 1c1zS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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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Components
#1: Protein | Mass: 37668.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: SLAFW is disordered in the electron densities of coordinates. EDQVDPRLIDGK is the purification tag. EDQVDPRLI is disordered in the electron densities of coordinates Source: (gene. exp.) ![]() ![]() | ||||||||
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#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 10.87 Å3/Da / Density % sol: 88.7 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM HEPES, 1.5 M AmSO4, 20 mM CaCl2 and 2% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 2, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→116.98 Å / Num. obs: 31543 / % possible obs: 98.8 % / Redundancy: 5 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1531 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1C1Z Resolution: 2.99→116.98 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.889 / SU B: 10.795 / SU ML: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.264 / ESU R Free: 0.23 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 197.31 Å2 / Biso mean: 75.41 Å2 / Biso min: 30 Å2
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Refinement step | Cycle: final / Resolution: 2.99→116.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.99→3.06 Å
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