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Yorodumi- PDB-3em0: Crystal structure of Zebrafish Ileal Bile Acid-Bindin Protein com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3em0 | ||||||
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Title | Crystal structure of Zebrafish Ileal Bile Acid-Bindin Protein complexed with cholic acid (crystal form B). | ||||||
Components | Ileal Bile Acid-Binding Protein | ||||||
Keywords | LIPID BINDING PROTEIN / Ileal bile acid-binding protein / zebrafish (Danio rerio) / cholic acid / Lipid-binding / Transport | ||||||
Function / homology | Function and homology information Recycling of bile acids and salts / Triglyceride catabolism / bile acid binding / fatty acid transport / fatty acid binding / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Danio rerio (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Capaldi, S. / Saccomani, G. / Fessas, D. / Signorelli, M. / Perduca, M. / Monaco, H.L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: The X-Ray structure of zebrafish (Danio rerio) ileal bile acid-binding protein reveals the presence of binding sites on the surface of the protein molecule. Authors: Capaldi, S. / Saccomani, G. / Fessas, D. / Signorelli, M. / Perduca, M. / Monaco, H.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3em0.cif.gz | 71.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3em0.ent.gz | 54.2 KB | Display | PDB format |
PDBx/mmJSON format | 3em0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/3em0 ftp://data.pdbj.org/pub/pdb/validation_reports/em/3em0 | HTTPS FTP |
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-Related structure data
Related structure data | 3elxC 3elzSC 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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2 |
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Unit cell |
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Details | The biological assembly is the protein monomer. |
-Components
#1: Protein | Mass: 15191.230 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: fabp6, zgc:92421 / Plasmid: pQE50 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: Q6IMW5 #2: Chemical | ChemComp-CHD / #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: 4.02 Å3/Da / Density % sol: 69.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M Sodium HEPES, 2.0 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.03 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 1, 2006 / Details: Double crystal (Si111, Si220) |
Radiation | Monochromator: Three-segment Pt-coated toroidal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. all: 24125 / Num. obs: 24125 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 43.6 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 1.3 / Num. unique all: 2395 / Rsym value: 0.312 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ELZ Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.927 / SU B: 10.728 / SU ML: 0.143 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.215 / ESU R Free: 0.185 / 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 mean: 38.977 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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