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Yorodumi- PDB-2yg2: Structure of apolioprotein M in complex with Sphingosine 1-Phosphate -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yg2 | ||||||
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Title | Structure of apolioprotein M in complex with Sphingosine 1-Phosphate | ||||||
Components | APOLIPOPROTEIN MAPOM | ||||||
Keywords | LIPID TRANSPORT / LIPOCALIN / HDL | ||||||
Function / homology | Function and homology information negative regulation of plasma lipoprotein oxidation / discoidal high-density lipoprotein particle / spherical high-density lipoprotein particle / lipid transporter activity / high-density lipoprotein particle remodeling / high-density lipoprotein particle clearance / low-density lipoprotein particle / reverse cholesterol transport / high-density lipoprotein particle assembly / very-low-density lipoprotein particle ...negative regulation of plasma lipoprotein oxidation / discoidal high-density lipoprotein particle / spherical high-density lipoprotein particle / lipid transporter activity / high-density lipoprotein particle remodeling / high-density lipoprotein particle clearance / low-density lipoprotein particle / reverse cholesterol transport / high-density lipoprotein particle assembly / very-low-density lipoprotein particle / lipoprotein metabolic process / high-density lipoprotein particle / cholesterol efflux / antioxidant activity / Retinoid metabolism and transport / cholesterol homeostasis / phospholipid binding / extracellular region Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Christoffersen, C. / Obinata, H. / Gowda, S. / Galvani, S. / Ahnstrom, J. / Sevvana, M. / Egerer-Sieber, C. / Muller, Y.A. / Hla, T. / Nielsen, L. / Dahlback, B. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Endothelium-Protective Sphingosine-1-Phosphate Provided by Hdl-Associated Apolipoprotein M. Authors: Christoffersen, C. / Obinata, H. / Kumaraswamy, S.B. / Galvani, S. / Ahnstrom, J. / Sevvana, M. / Egerer-Sieber, C. / Muller, Y.A. / Hla, T. / Nielsen, L.B. / Dahlback, B. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yg2.cif.gz | 145.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yg2.ent.gz | 114.8 KB | Display | PDB format |
PDBx/mmJSON format | 2yg2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/2yg2 ftp://data.pdbj.org/pub/pdb/validation_reports/yg/2yg2 | HTTPS FTP |
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-Related structure data
Related structure data | 2wewS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 19242.789 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O95445 #2: Chemical | #3: Chemical | ChemComp-FLC / | #4: 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 | Density Matthews: 2.46 Å3/Da / Density % sol: 49.98 % / Description: NONE |
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Crystal grow | Details: 0.15 M LITHIUM SULFATE MONOHYDRATE, 0.1 M CITRIC ACID PH 3.5, 18 % W/V PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 4, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→25 Å / Num. obs: 40599 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 6.07 % / Biso Wilson estimate: 29.02 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 6.18 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 3.34 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WEW Resolution: 1.7→34.14 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.551 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.551 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→34.14 Å
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