+Open data
-Basic information
Entry | Database: PDB / ID: 2xkl | ||||||
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Title | Crystal Structure of Mouse Apolipoprotein M | ||||||
Components | APOLIPOPROTEIN MAPOM | ||||||
Keywords | LIPID TRANSPORT | ||||||
Function / homology | Function and homology information negative regulation of plasma lipoprotein oxidation / Retinoid metabolism and transport / spherical high-density lipoprotein particle / discoidal high-density lipoprotein particle / lipid transporter activity / lipoprotein metabolic process / high-density lipoprotein particle remodeling / high-density lipoprotein particle clearance / low-density lipoprotein particle / reverse cholesterol transport ...negative regulation of plasma lipoprotein oxidation / Retinoid metabolism and transport / spherical high-density lipoprotein particle / discoidal high-density lipoprotein particle / lipid transporter activity / lipoprotein metabolic process / 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 / high-density lipoprotein particle / cholesterol efflux / antioxidant activity / response to glucose / phospholipid binding / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Sevvana, M. / Kassler, K. / Josefin, A. / Weiler, S. / Dahlback, B. / Sticht, H. / Muller, Y.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Mouse Apom Displays an Unprecedented Seven-Stranded Lipocalin Fold: Folding Decoy or Alternative Native Fold? Authors: Sevvana, M. / Kassler, K. / Ahnstrom, J. / Weiler, S. / Dahlback, B. / Sticht, H. / Muller, Y.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xkl.cif.gz | 76.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xkl.ent.gz | 56.1 KB | Display | PDB format |
PDBx/mmJSON format | 2xkl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xk/2xkl ftp://data.pdbj.org/pub/pdb/validation_reports/xk/2xkl | 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 19101.688 Da / Num. of mol.: 1 / Fragment: RESIDUES 20-190 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET30XA/LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9Z1R3 |
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-Non-polymers , 5 types, 97 molecules
#2: Chemical | ChemComp-GOL / |
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#3: Chemical | ChemComp-POL / |
#4: Chemical | ChemComp-EDO / |
#5: Chemical | ChemComp-NA / |
#6: 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: 2.28 Å3/Da / Density % sol: 46.02 % / Description: NONE |
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Crystal grow | pH: 5.6 Details: 0.1 M NA CITRATE PH 5.6, 20% V/V 2-PROPANOL, 20% W/V PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Type: BESSY / Wavelength: 0.9184 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 6802 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Biso Wilson estimate: 26.489 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 10.84 |
Reflection shell | Resolution: 2.5→2.65 Å / Redundancy: 8.08 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.56 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WEW Resolution: 2.5→19.94 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.88 / SU B: 16.247 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.46 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.554 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→19.94 Å
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Refine LS restraints |
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