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Yorodumi- PDB-6xst: Recombinant Beta-2-Glycoprotein I with putative membrane insertio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xst | ||||||
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Title | Recombinant Beta-2-Glycoprotein I with putative membrane insertion loop | ||||||
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 / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å | ||||||
Authors | Klenotic, P.A. / Yu, E.W.Y. | ||||||
Citation | Journal: To Be Published Title: Beta-2-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 | 6xst.cif.gz | 146.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xst.ent.gz | 115.7 KB | Display | PDB format |
PDBx/mmJSON format | 6xst.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xst_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6xst_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6xst_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 6xst_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xs/6xst ftp://data.pdbj.org/pub/pdb/validation_reports/xs/6xst | HTTPS FTP |
-Related structure data
Related structure data | 7jikC 1qubS S: Starting model for refinement C: citing same article (ref.) |
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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 genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: APOH, B2G1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P02749 | ||
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#2: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#4: 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 | Method: vapor diffusion, hanging drop / Details: 100mM Hepes, pH 7.5, 1.8M Ammonium Sulfate |
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-Data collection
Diffraction | Mean temperature: 277 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.91→100 Å / Num. obs: 34541 / % possible obs: 99.7 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.206 / Rpim(I) all: 0.081 / Rrim(I) all: 0.222 / Χ2: 1 / Net I/σ(I): 3.8 / Num. measured all: 253404 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.92→87.61 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.83 / 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: 189.82 Å2 / Biso mean: 88.6605 Å2 / Biso min: 30 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.92→87.61 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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