+Open data
-Basic information
Entry | Database: PDB / ID: 1a2d | ||||||
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Title | PYRIDOXAMINE MODIFIED MURINE ADIPOCYTE LIPID BINDING PROTEIN | ||||||
Components | ADIPOCYTE LIPID BINDING PROTEIN | ||||||
Keywords | FATTY ACID BINDING PROTEIN / TRANSPORT / PHOSPHORYLATION | ||||||
Function / homology | Function and homology information Triglyceride catabolism / hormone receptor binding / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid binding / cellular response to lithium ion / white fat cell differentiation / long-chain fatty acid transport / fatty acid transport / brown fat cell differentiation / cholesterol homeostasis ...Triglyceride catabolism / hormone receptor binding / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid binding / cellular response to lithium ion / white fat cell differentiation / long-chain fatty acid transport / fatty acid transport / brown fat cell differentiation / cholesterol homeostasis / fatty acid metabolic process / fatty acid binding / response to bacterium / positive regulation of inflammatory response / cellular response to tumor necrosis factor / positive regulation of cold-induced thermogenesis / 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 / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Ory, J. / Mazhary, A. / Kuang, H. / Davies, R. / Distefano, M. / Banaszak, L. | ||||||
Citation | Journal: Protein Eng. / Year: 1998 Title: Structural characterization of two synthetic catalysts based on adipocyte lipid-binding protein. Authors: Ory, J.J. / Mazhary, A. / Kuang, H. / Davies, R.R. / Distefano, M.D. / Banaszak, L.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a2d.cif.gz | 58.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a2d.ent.gz | 47 KB | Display | PDB format |
PDBx/mmJSON format | 1a2d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/1a2d ftp://data.pdbj.org/pub/pdb/validation_reports/a2/1a2d | HTTPS FTP |
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-Related structure data
Related structure data | 1a18C 1libS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 14721.933 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: PROTEIN MODIFIED BY REACTION WITH 5-(2-PYRIDYLDITHIO)PYRIDOXAMINE Source: (gene. exp.) Mus musculus (house mouse) / Description: SEE KUANG ET AL., JACS 118\:10702-10706 (1996) / Cell: ADIPOCYTE / Production host: Escherichia coli (E. coli) / References: UniProt: P04117 #2: Chemical | #3: 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: 3.4 Å3/Da / Density % sol: 64.4 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Jun 1, 1996 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→25 Å / Num. obs: 7640 / % possible obs: 91.7 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rsym value: 0.078 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.37→2.52 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.325 / % possible all: 62.4 |
Reflection | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Num. obs: 8916 / % possible obs: 94 % / Num. measured all: 76938 / Rmerge(I) obs: 0.0946 |
Reflection shell | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 2.75 Å / % possible obs: 78.05 % / Rmerge(I) obs: 0.3021 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LIB Resolution: 2.4→25 Å / Rfactor Rfree error: 0.0124 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 2.4→25 Å
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LS refinement shell | Resolution: 2.4→2.51 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.843C / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.285 / Rfactor Rwork: 0.186 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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