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Yorodumi- PDB-4azo: Murine epidermal fatty acid-binding protein (FABP5), apo form, po... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4azo | ||||||
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Title | Murine epidermal fatty acid-binding protein (FABP5), apo form, poly- his tag removed | ||||||
Components | FATTY ACID-BINDING PROTEIN, EPIDERMAL | ||||||
Keywords | LIPID BINDING PROTEIN / LIPID CARRIER PROTEIN / BETA-BARREL / BETA-CLAMSHELL / DOMAIN SWAPPING | ||||||
Function / homology | Function and homology information Signaling by Retinoic Acid / regulation of prostaglandin biosynthetic process / regulation of retrograde trans-synaptic signaling by endocanabinoid / Triglyceride catabolism / lipid transport across blood-brain barrier / positive regulation of peroxisome proliferator activated receptor signaling pathway / negative regulation of glucose transmembrane transport / regulation of sensory perception of pain / phosphatidylcholine biosynthetic process / retinoic acid binding ...Signaling by Retinoic Acid / regulation of prostaglandin biosynthetic process / regulation of retrograde trans-synaptic signaling by endocanabinoid / Triglyceride catabolism / lipid transport across blood-brain barrier / positive regulation of peroxisome proliferator activated receptor signaling pathway / negative regulation of glucose transmembrane transport / regulation of sensory perception of pain / phosphatidylcholine biosynthetic process / retinoic acid binding / long-chain fatty acid transmembrane transporter activity / fatty acid transport / Neutrophil degranulation / fatty acid binding / lipid metabolic process / glucose metabolic process / glucose homeostasis / positive regulation of cold-induced thermogenesis / postsynaptic density / synapse / extracellular space / extracellular region / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å | ||||||
Authors | Sanson, B. / Wang, T. / Sun, J. / Kaczocha, M. / Ojima, I. / Deutsch, D. / Li, H. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Crystallographic Study of Fabp5 as an Intracellular Endocannabinoid Transporter. Authors: Sanson, B. / Wang, T. / Sun, J. / Wang, L. / Kaczocha, M. / Ojima, I. / Deutsch, D. / Li, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4azo.cif.gz | 68.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4azo.ent.gz | 50.9 KB | Display | PDB format |
PDBx/mmJSON format | 4azo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4azo_validation.pdf.gz | 428 KB | Display | wwPDB validaton report |
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Full document | 4azo_full_validation.pdf.gz | 429.1 KB | Display | |
Data in XML | 4azo_validation.xml.gz | 7.5 KB | Display | |
Data in CIF | 4azo_validation.cif.gz | 9.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/4azo ftp://data.pdbj.org/pub/pdb/validation_reports/az/4azo | HTTPS FTP |
-Related structure data
Related structure data | 4azmC 4aznC 4azpC 4azqC 4azrC 1b56S 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
#1: Protein | Mass: 15454.736 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Tissue: EPIDERMIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q497I3, UniProt: Q05816*PLUS |
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#2: Chemical | ChemComp-CL / |
#3: 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: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 200 MM NACL, 50 MM NAAC PH 4.8, 25% PEG3350 AND 5% MPD, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K. CRYPROTECION: 25% GLYCEROL IN MOTHER LIQUOR. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 14, 2010 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→20 Å / Num. obs: 6932 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 10.6 % / Biso Wilson estimate: 71.5 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 33.1 |
Reflection shell | Resolution: 2.33→2.4 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4 / % possible all: 98.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1B56 Resolution: 2.33→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.924 / SU B: 18.071 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.373 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THERE IS WEAK DENSITY IN THE BINDING POCKET, LIKELY DUE TO THE INCOMPLETE DELIPIDATION OF FABP. THE DENSITY FOR THE POTENTIAL RESIDUAL ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THERE IS WEAK DENSITY IN THE BINDING POCKET, LIKELY DUE TO THE INCOMPLETE DELIPIDATION OF FABP. THE DENSITY FOR THE POTENTIAL RESIDUAL LIPID IS TOO WEAK TO BE MODELED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.393 Å2
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Refinement step | Cycle: LAST / Resolution: 2.33→20 Å
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Refine LS restraints |
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