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Yorodumi- PDB-1qub: CRYSTAL STRUCTURE OF THE GLYCOSYLATED FIVE-DOMAIN HUMAN BETA2-GLY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qub | |||||||||
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Title | CRYSTAL STRUCTURE OF THE GLYCOSYLATED FIVE-DOMAIN HUMAN BETA2-GLYCOPROTEIN I PURIFIED FROM BLOOD PLASMA | |||||||||
Components | PROTEIN (human beta2-Glycoprotein I) | |||||||||
Keywords | MEMBRANE ADHESION / SHORT CONSENSUS REPEAT / SUSHI / COMPLEMENT CONTROL PROTEIN / N-GLYCOSYLATION / MULTI-DOMAIN | |||||||||
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 / MIRAS / Resolution: 2.7 Å | |||||||||
Authors | Bouma, B. / de Groot, P.G. / van den Elsen, J.M.H. / Ravelli, R.B.G. / Schouten, A. / Simmelink, M.J.A. / Derksen, R.H.W.M. / Kroon, J. / Gros, P. | |||||||||
Citation | Journal: EMBO J. / Year: 1999 Title: Adhesion mechanism of human beta(2)-glycoprotein I to phospholipids based on its crystal structure. Authors: Bouma, B. / de Groot, P.G. / van den Elsen, J.M. / Ravelli, R.B. / Schouten, A. / Simmelink, M.J. / Derksen, R.H. / Kroon, J. / Gros, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qub.cif.gz | 74.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qub.ent.gz | 58.9 KB | Display | PDB format |
PDBx/mmJSON format | 1qub.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qub_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1qub_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1qub_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 1qub_validation.cif.gz | 19.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qu/1qub ftp://data.pdbj.org/pub/pdb/validation_reports/qu/1qub | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35478.641 Da / Num. of mol.: 1 / Fragment: BETA2-GLYCOPROTEIN I / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organelle: BLOOD PLASMA / References: UniProt: P02749 | ||
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#2: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-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)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#4: Sugar | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 8.5 Å3/Da / Density % sol: 86 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.5 M ammonium sulphate 20 mM cadmium chloride 2 % (v/v) glycerol 100 mM HEPES 1.5 M AMMONIUM PHOSPHATE 100 MM SODIUM ACETATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.3 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9354 |
Detector | Type: ADSC / Detector: CCD / Date: Sep 27, 1998 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SI(333) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9354 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→40 Å / Num. all: 42497 / Num. obs: 42497 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 46.7 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 2 / Num. unique all: 6122 / Rsym value: 0.364 / % possible all: 99.6 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 99.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.7→40 Å / Rfactor Rfree error: 0.006 / Rfactor Rfree error details: 0.006 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Used maximum likelihood target using amplitudes
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.7939 Å2 / ksol: 0.371246 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 40 Å / σ(F): 0 / % reflection Rfree: 4.9 % | ||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 51.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.399 / % reflection Rfree: 5.2 % / Rfactor Rwork: 0.399 |