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Yorodumi- PDB-2ft9: Crystal structure of axolotl (Ambystoma mexicanum) liver bile aci... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ft9 | ||||||
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Title | Crystal structure of axolotl (Ambystoma mexicanum) liver bile acid-binding protein bound to cholic acid | ||||||
Components | Fatty acid-binding protein 2, liver | ||||||
Keywords | LIPID BINDING PROTEIN / liver bile acid-binding protein / liver basic fatty acid-binding protein / axolotl / cholic acid | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Ambystoma mexicanum (axolotl) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Capaldi, S. / Guariento, M. / Perduca, M. / Di Pietro, S.M. / Santome, J.A. / Monaco, H.L. | ||||||
Citation | Journal: Proteins / Year: 2006 Title: Crystal structure of axolotl (Ambystoma mexicanum) liver bile acid-binding protein bound to cholic and oleic acid Authors: Capaldi, S. / Guariento, M. / Perduca, M. / Di Pietro, S.M. / Santome, J.A. / Monaco, H.L. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Crystallization and preliminary X-ray study of two liver basic fatty acid-binding proteins Authors: Di Pietro, S.M. / Perduca, M. / Santome, J.A. / 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 | 2ft9.cif.gz | 37.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ft9.ent.gz | 25.7 KB | Display | PDB format |
PDBx/mmJSON format | 2ft9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/2ft9 ftp://data.pdbj.org/pub/pdb/validation_reports/ft/2ft9 | HTTPS FTP |
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-Related structure data
Related structure data | 2ftbSC 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: 13758.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ambystoma mexicanum (axolotl) / Tissue: liver / References: UniProt: P81400 |
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#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: 1.6M sodium citrate, 0.1M hepes, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 15, 2005 |
Radiation | Monochromator: Si 311 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→47.25 Å / Num. obs: 5508 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.065 |
Reflection shell | Resolution: 2.5→2.56 Å / Rsym value: 0.14 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2FTB Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.816 / SU B: 14.506 / SU ML: 0.311 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.626 / ESU R Free: 0.36 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.5 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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