[English] 日本語
Yorodumi- PDB-3stm: Structure of human LFABP in complex with one molecule of palmitic acid -
+Open data
-Basic information
Entry | Database: PDB / ID: 3stm | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of human LFABP in complex with one molecule of palmitic acid | ||||||
Components | Fatty acid-binding protein, liver | ||||||
Keywords | LIPID BINDING PROTEIN / LFABP / Palmitic acid / Fatty acid binding | ||||||
Function / homology | Function and homology information response to vitamin B3 / oleic acid binding / apical cortex / positive regulation of fatty acid beta-oxidation / bile acid binding / intestinal absorption / Heme degradation / long-chain fatty acid transmembrane transporter activity / heterocyclic compound binding / Triglyceride catabolism ...response to vitamin B3 / oleic acid binding / apical cortex / positive regulation of fatty acid beta-oxidation / bile acid binding / intestinal absorption / Heme degradation / long-chain fatty acid transmembrane transporter activity / heterocyclic compound binding / Triglyceride catabolism / antioxidant activity / peroxisomal matrix / fatty acid transport / Regulation of lipid metabolism by PPARalpha / fatty acid binding / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / phospholipid binding / PPARA activates gene expression / Cytoprotection by HMOX1 / cellular response to hydrogen peroxide / cellular response to hypoxia / chromatin binding / negative regulation of apoptotic process / protein-containing complex / extracellular exosome / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.216 Å | ||||||
Authors | Sharma, A. / Sharma, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Fatty acid induced remodeling within the Human liver fatty acid binding protein Authors: Sharma, A. / Sharma, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3stm.cif.gz | 39.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3stm.ent.gz | 26.1 KB | Display | PDB format |
PDBx/mmJSON format | 3stm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/st/3stm ftp://data.pdbj.org/pub/pdb/validation_reports/st/3stm | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 14599.728 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FABP1, FABPL / Production host: Escherichia coli (E. coli) / References: UniProt: P07148 |
---|---|
#2: Chemical | ChemComp-PLM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.37 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.15 M potassium bromide and 30% polyethylene glycol monomethyl ether (PEG MME) 2000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 7, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.216→28.011 Å / Num. obs: 6817 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.21→2.29 Å / Redundancy: 5 % / Rmerge(I) obs: 0.45 / % possible all: 86.5 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.216→19.176 Å / Occupancy max: 1 / Occupancy min: 0.48 / FOM work R set: 0.7322 / SU ML: 0.33 / σ(F): 1.35 / Phase error: 31.81 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.744 Å2 / ksol: 0.278 e/Å3 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.31 Å2 / Biso mean: 40.3881 Å2 / Biso min: 23.85 Å2
| ||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.216→19.176 Å
| ||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2 / % reflection obs: 99 %
|