+Open data
-Basic information
Entry | Database: PDB / ID: 5l8n | ||||||
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Title | crystal structure of human FABP6 protein with fragment 1 | ||||||
Components | Gastrotropin | ||||||
Keywords | LIPID BINDING PROTEIN / FABP6 / Fatty acid binding protein 6 / Ileal bile acid binding protein / I-BABP / Ileal / Gastrotropin / Fragments | ||||||
Function / homology | Function and homology information NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / Triglyceride catabolism / fatty acid transport / Recycling of bile acids and salts / fatty acid binding / lipid metabolic process / negative regulation of cell population proliferation / lipid binding / membrane / nucleus ...NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / Triglyceride catabolism / fatty acid transport / Recycling of bile acids and salts / fatty acid binding / lipid metabolic process / negative regulation of cell population proliferation / lipid binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å | ||||||
Authors | Hendrick, A. / Mueller, I. / Leonard, P.M. / Davenport, R. / Mitchell, P. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2016 Title: Identification and Investigation of Novel Binding Fragments in the Fatty Acid Binding Protein 6 (FABP6). Authors: Hendrick, A.G. / Muller, I. / Willems, H. / Leonard, P.M. / Irving, S. / Davenport, R. / Ito, T. / Reeves, J. / Wright, S. / Allen, V. / Wilkinson, S. / Heffron, H. / Bazin, R. / Turney, J. / Mitchell, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l8n.cif.gz | 86.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l8n.ent.gz | 64.5 KB | Display | PDB format |
PDBx/mmJSON format | 5l8n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5l8n_validation.pdf.gz | 664.6 KB | Display | wwPDB validaton report |
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Full document | 5l8n_full_validation.pdf.gz | 668.1 KB | Display | |
Data in XML | 5l8n_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 5l8n_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l8/5l8n ftp://data.pdbj.org/pub/pdb/validation_reports/l8/5l8n | HTTPS FTP |
-Related structure data
Related structure data | 5l8iSC 5l8oC 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 14389.235 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FABP6, ILBP, ILLBP / Production host: Escherichia coli (E. coli) / References: UniProt: P51161 #2: Chemical | #3: Chemical | ChemComp-PEG / #4: Chemical | ChemComp-P33 / | #5: 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: 2.08 Å3/Da / Density % sol: 40.73 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 39% w/v PEG 3350 and 0.1 M Bis-tris pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→47.12 Å / Num. obs: 19956 / % possible obs: 99 % / Redundancy: 3.3 % / Biso Wilson estimate: 42.5 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.059 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.12→2.18 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.738 / Mean I/σ(I) obs: 1.6 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5L8I Resolution: 2.12→47.12 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.899 / SU B: 9.799 / SU ML: 0.242 / Cross valid method: THROUGHOUT / ESU R: 0.335 / ESU R Free: 0.259 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.757 Å2
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Refinement step | Cycle: 1 / Resolution: 2.12→47.12 Å
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Refine LS restraints |
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