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Yorodumi- PDB-3jsq: Crystal structure of adipocyte fatty acid binding protein non-cov... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jsq | ||||||
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Title | Crystal structure of adipocyte fatty acid binding protein non-covalently modified with 4-hydroxy-2-nonenal | ||||||
Components | Adipocyte fatty acid-binding protein | ||||||
Keywords | LIPID BINDING PROTEIN / fatty acid binding protein | ||||||
Function / homology | Function and homology information Triglyceride catabolism / hormone receptor binding / long-chain fatty acid transmembrane transporter activity / cellular response to lithium ion / long-chain fatty acid binding / white fat cell differentiation / long-chain fatty acid transport / brown fat cell differentiation / fatty acid transport / cholesterol homeostasis ...Triglyceride catabolism / hormone receptor binding / long-chain fatty acid transmembrane transporter activity / cellular response to lithium ion / long-chain fatty acid binding / white fat cell differentiation / long-chain fatty acid transport / brown fat cell differentiation / fatty acid transport / cholesterol homeostasis / fatty acid metabolic process / fatty acid binding / response to bacterium / positive regulation of inflammatory response / positive regulation of cold-induced thermogenesis / cellular response to tumor necrosis factor / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Hellberg, K. / Grimsrud, P.A. / Kruse, A.C. / Banaszak, L.J. / Ohlendorf, D.H. / Bernlohr, D.A. | ||||||
Citation | Journal: Protein Sci. / Year: 2010 Title: X-ray crystallographic analysis of adipocyte fatty acid binding protein (aP2) modified with 4-hydroxy-2-nonenal. Authors: Hellberg, K. / Grimsrud, P.A. / Kruse, A.C. / Banaszak, L.J. / Ohlendorf, D.H. / Bernlohr, D.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3jsq.cif.gz | 41.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jsq.ent.gz | 28.6 KB | Display | PDB format |
PDBx/mmJSON format | 3jsq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jsq_validation.pdf.gz | 450.8 KB | Display | wwPDB validaton report |
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Full document | 3jsq_full_validation.pdf.gz | 451.9 KB | Display | |
Data in XML | 3jsq_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 3jsq_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/js/3jsq ftp://data.pdbj.org/pub/pdb/validation_reports/js/3jsq | HTTPS FTP |
-Related structure data
Related structure data | 3js1C 1lieS C: citing same article (ref.) 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 on special symmetry positions |
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Details | Authors state that the assembly is a dimer. The second part of the biological assembly is generated by the two fold axis: [-X,Y,1/2-Z] as shown in remark 350 |
-Components
#1: Protein | Mass: 14539.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fabp4, Ap2 / Plasmid: Modified pRSETb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P04117 | ||
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#2: Chemical | ChemComp-CL / | ||
#3: Chemical | ChemComp-HNE / ( | ||
#4: Chemical | ChemComp-PO4 / #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: 3.05 Å3/Da / Density % sol: 59.72 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES, 1.6 M Sodium/potassium phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97934 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 29, 2008 / Details: Mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 7758 / Num. obs: 7758 / % possible obs: 93.7 % / Redundancy: 3.6 % / Rsym value: 0.065 / Net I/σ(I): 16.63 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.85 / Num. unique all: 297 / Rsym value: 0.332 / % possible all: 73.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1LIE Resolution: 2.3→19.97 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.904 / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.325 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 max: 96.42 Å2 / Biso mean: 34.676 Å2 / Biso min: 16.97 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→19.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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