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- PDB-4y0r: Bovine beta-lactoglobulin complex with pramocaine crystallized fr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4y0r | ||||||
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Title | Bovine beta-lactoglobulin complex with pramocaine crystallized from ammonium sulphate (BLG-PRM2) | ||||||
![]() | Beta-lactoglobulin | ||||||
![]() | TRANSPORT / LIGAND BINDING | ||||||
Function / homology | ![]() retinol binding / long-chain fatty acid binding / extracellular space / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Loch, J.I. / Bonarek, P. / Polit, A. / Jablonski, M. / Czub, M. / Ye, X. / Lewinski, K. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 46.6 KB | Display | ![]() |
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PDB format | ![]() | 31.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 606.7 KB | Display | ![]() |
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Full document | ![]() | 607.7 KB | Display | |
Data in XML | ![]() | 8.9 KB | Display | |
Data in CIF | ![]() | 11.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4y0pC ![]() 4y0qC ![]() 4y0sC ![]() 1bsyS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 18301.174 Da / Num. of mol.: 1 / Fragment: unp residues 17-178 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Chemical | ChemComp-PX9 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: protein 20 mg/ml, 2.4 M (NH4)2SO4 in 0.5 M Tris-HCl pH 8.9 and 5 mM pramociane |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SEALED TUBE / Type: OTHER / Wavelength: 1.54 Å |
Detector | Type: AGILENT ATLAS CCD / Detector: CCD / Date: Apr 29, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→13.43 Å / Num. obs: 8567 / % possible obs: 98.9 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 2.6 / % possible all: 96.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1BSY Resolution: 2.3→13.43 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.897 / SU B: 9.054 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.384 / ESU R Free: 0.287 / 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: 38.45 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→13.43 Å
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Refine LS restraints |
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