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Yorodumi- PDB-6gf9: Thermodynamic, Crystallographic and Computational Studies of Non ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gf9 | ||||||
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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 / MOLECULAR REPLACEMENT / Resolution: 2.1 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 | 6gf9.cif.gz | 78.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gf9.ent.gz | 63 KB | Display | PDB format |
PDBx/mmJSON format | 6gf9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gf9_validation.pdf.gz | 613.6 KB | Display | wwPDB validaton report |
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Full document | 6gf9_full_validation.pdf.gz | 615.4 KB | Display | |
Data in XML | 6gf9_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 6gf9_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gf/6gf9 ftp://data.pdbj.org/pub/pdb/validation_reports/gf/6gf9 | 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 natural source / Details: protein / Source: (natural) Bos taurus (cattle) / Tissue: milk / References: UniProt: P02754 |
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#2: Chemical | ChemComp-X90 / |
#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: 52.12 % |
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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: PX14.2 / Wavelength: 0.932 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 21, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.932 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→10 Å / Num. obs: 11533 / % possible obs: 91.4 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 9.3 |
Reflection shell | Highest resolution: 2.1 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→9.99 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 12.166 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.251 / ESU R Free: 0.205 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.573 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→9.99 Å
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Refine LS restraints |
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