+Open data
-Basic information
Entry | Database: PDB / ID: 2wew | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human apoM in complex with myristic acid | ||||||
Components | APOLIPOPROTEIN M | ||||||
Keywords | LIPID TRANSPORT / LIGAND-BINDING SPECIFICITY / GLYCOPROTEIN / MYRISTIC ACID / HDL / LIPOCALIN / TRANSPORT / LIPOPROTEINS | ||||||
Function / homology | Function and homology information negative regulation of plasma lipoprotein oxidation / spherical high-density lipoprotein particle / discoidal high-density lipoprotein particle / lipoprotein metabolic process / high-density lipoprotein particle clearance / high-density lipoprotein particle remodeling / lipid transporter activity / reverse cholesterol transport / high-density lipoprotein particle assembly / very-low-density lipoprotein particle ...negative regulation of plasma lipoprotein oxidation / spherical high-density lipoprotein particle / discoidal high-density lipoprotein particle / lipoprotein metabolic process / high-density lipoprotein particle clearance / high-density lipoprotein particle remodeling / lipid transporter activity / reverse cholesterol transport / high-density lipoprotein particle assembly / very-low-density lipoprotein particle / low-density lipoprotein particle / 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 / MAD / Resolution: 1.95 Å | ||||||
Authors | Sevvana, M. / Ahnstrom, J. / Egerer-Sieber, C. / Dahlback, B. / Muller, Y.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Serendipitous Fatty Acid Binding Reveals the Structural Determinants for Ligand Recognition in Apolipoprotein M. Authors: Sevvana, M. / Ahnstrom, J. / Egerer-Sieber, C. / Lange, H.A. / Dahlback, B. / Muller, Y.A. | ||||||
History |
| ||||||
Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2wew.cif.gz | 81.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2wew.ent.gz | 66.6 KB | Display | PDB format |
PDBx/mmJSON format | 2wew.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wew_validation.pdf.gz | 444.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2wew_full_validation.pdf.gz | 447.8 KB | Display | |
Data in XML | 2wew_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 2wew_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/we/2wew ftp://data.pdbj.org/pub/pdb/validation_reports/we/2wew | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 19242.789 Da / Num. of mol.: 1 / Fragment: RESIDUES 22-188 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O95445 |
---|---|
#2: Chemical | ChemComp-MYR / |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
Sequence details | RESIDUES 22-188 WITHOUT SIGNAL PEPTIDE HAVE BEEN CLONED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.56 % / Description: NONE |
---|---|
Crystal grow | pH: 7.2 Details: ABOUT 1-2 MICROL OF PROTEIN (10-16 MG/ML IN 20 MM TRIS-HCL, PH 7.2) WERE MIXED WITH 1-2 MICROL OF 30 % PEG1500 (W/V, IN DEIONISED WATER) AND EQUILIBRATED AGAINST 700 MICROL OF RESERVOIR ...Details: ABOUT 1-2 MICROL OF PROTEIN (10-16 MG/ML IN 20 MM TRIS-HCL, PH 7.2) WERE MIXED WITH 1-2 MICROL OF 30 % PEG1500 (W/V, IN DEIONISED WATER) AND EQUILIBRATED AGAINST 700 MICROL OF RESERVOIR SOLUTION CONTAINING 30 % PEG1500. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 |
Detector | Type: RAYONICS / Detector: CCD |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→20 Å / Num. obs: 13952 / % possible obs: 98.4 % / Observed criterion σ(I): 3 / Redundancy: 7.06 % / Biso Wilson estimate: 36.55 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 25.18 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.84 / % possible all: 91.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.916 / SU B: 9.076 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.36 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|