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Yorodumi- PDB-4y0q: Bovine beta-lactoglobulin complex with pramocaine crystallized fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4y0q | |||||||||
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Title | Bovine beta-lactoglobulin complex with pramocaine crystallized from sodium citrate (BLG-PRM1) | |||||||||
Components | Beta-lactoglobulin | |||||||||
Keywords | TRANSPORT PROTEIN / LIGAND BINDING | |||||||||
Function / homology | Function and homology information retinol binding / long-chain fatty acid binding / extracellular region / identical protein binding Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Loch, J.I. / Bonarek, P. / Polit, A. / Jablonski, M. / Czub, M. / Ye, X. / Lewinski, K. | |||||||||
Funding support | Poland, 1items
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Citation | Journal: Int.J.Biol.Macromol. / Year: 2015 Title: beta-Lactoglobulin interactions with local anaesthetic drugs - Crystallographic and calorimetric studies. Authors: Loch, J.I. / Bonarek, P. / Polit, A. / Jabonski, M. / Czub, M. / Ye, X. / Lewinski, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y0q.cif.gz | 47.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y0q.ent.gz | 32.2 KB | Display | PDB format |
PDBx/mmJSON format | 4y0q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4y0q_validation.pdf.gz | 609.3 KB | Display | wwPDB validaton report |
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Full document | 4y0q_full_validation.pdf.gz | 609.7 KB | Display | |
Data in XML | 4y0q_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 4y0q_validation.cif.gz | 11.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y0/4y0q ftp://data.pdbj.org/pub/pdb/validation_reports/y0/4y0q | HTTPS FTP |
-Related structure data
Related structure data | 4y0pC 4y0rC 4y0sC 1bsyS 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: 18301.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P02754 |
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#2: Chemical | ChemComp-PX9 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: protein 20 mg/ml, 1.34 M sodium citrate in 0.1 M Tris-HCl pH 7.5 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SEALED TUBE / Type: Agilent SuperNova / Wavelength: 1.54 Å |
Detector | Type: AGILENT ATLAS CCD / Detector: CCD / Date: Apr 23, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→13.29 Å / Num. obs: 12846 / % possible obs: 99.1 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 1.9 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1bsy Resolution: 2→13.29 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.436 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.197 / 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: 38.524 Å2
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Refinement step | Cycle: 1 / Resolution: 2→13.29 Å
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Refine LS restraints |
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