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Yorodumi- PDB-6ge7: Thermodynamic, Crystallographic and Computational Studies of Non ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ge7 | ||||||
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Title | Thermodynamic, Crystallographic and Computational Studies of Non Mammalian Fatty Acid Binding to Bovine b-Lactoglobulin | ||||||
Components | Beta-lactoglobulin | ||||||
Keywords | TRANSPORT PROTEIN / lactoglobulin / fatty acid / Non-Mammalian | ||||||
Function / homology | Function and homology information retinol binding / long-chain fatty acid binding / extracellular space / identical protein binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å | ||||||
Authors | Kontopidis, G. / Rovoli, M. | ||||||
Citation | Journal: Int. J. Biol. Macromol. / Year: 2018 Title: Thermodynamic, crystallographic and computational studies of non-mammalian fatty acid binding to bovine beta-Lactoglobulin. Authors: Rovoli, M. / Thireou, T. / Choiset, Y. / Haertle, T. / Sawyer, L. / Eliopoulos, E. / Kontopidis, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ge7.cif.gz | 78.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ge7.ent.gz | 63.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ge7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ge7_validation.pdf.gz | 598.9 KB | Display | wwPDB validaton report |
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Full document | 6ge7_full_validation.pdf.gz | 600.7 KB | Display | |
Data in XML | 6ge7_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 6ge7_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ge/6ge7 ftp://data.pdbj.org/pub/pdb/validation_reports/ge/6ge7 | HTTPS FTP |
-Related 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: 18301.174 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: LGB / Production host: Bos taurus (cattle) / Tissue (production host): milk / References: UniProt: P02754 |
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#2: Chemical | ChemComp-EW8 / |
#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: 2.57 Å3/Da / Density % sol: 52.22 % |
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Crystal grow | Temperature: 293.2 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: protein 20 mg/mL, ligand 10mM, 20mM Tris buffer, pH 8, which were mixed with 4 microliter of well solution. Drops were equilibrated against 1 mL of well solution containing 1.43 M sodium ...Details: protein 20 mg/mL, ligand 10mM, 20mM Tris buffer, pH 8, which were mixed with 4 microliter of well solution. Drops were equilibrated against 1 mL of well solution containing 1.43 M sodium citrate and 0.1M Hepes, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 1.2 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 27, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→25 Å / Num. obs: 8916 / % possible obs: 98.9 % / Redundancy: 9.4 % / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 2.3→2.34 Å / Num. unique obs: 435 |
-Processing
Software |
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Refinement | Resolution: 2.3→24.33 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 13.533 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.326 / ESU R Free: 0.24 / 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: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.083 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→24.33 Å
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Refine LS restraints |
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