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Open data
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Basic information
Entry | Database: PDB / ID: 6qpd | ||||||
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Title | Engineered beta-lactoglobulin: variant I56F | ||||||
![]() | Beta-lactoglobulin![]() | ||||||
![]() | ![]() ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Loch, J.I. / Kaczor, K. / Leiwnski, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-based design approach to rational site-directed mutagenesis of beta-lactoglobulin. Authors: Bonarek, P. / Loch, J.I. / Tworzydlo, M. / Cooper, D.R. / Milto, K. / Wrobel, P. / Kurpiewska, K. / 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 | ![]() | 50.8 KB | Display | ![]() |
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PDB format | ![]() | 34.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6qi6C ![]() 6qi7C ![]() 6qpeC ![]() 6rwpC ![]() 6rwqC ![]() 6rwrC ![]() 6rytC ![]() 6xveC ![]() 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | ![]() Mass: 18335.191 Da / Num. of mol.: 1 / Mutation: L1A, I2S, I56F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-SO4 / ![]() | ||
#3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.63 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.60 M (NH4)2SO4 in 0.1 M Tris-HCl pH 8.0 |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SEALED TUBE / Type: Agilent SuperNova / Wavelength: 1.5406 Å | ||||||||||||||||||||||||||||||
Detector | Type: AGILENT ATLAS CCD / Detector: CCD / Date: Feb 25, 2015 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2→13.81 Å / Num. obs: 12897 / % possible obs: 98.5 % / Redundancy: 2.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.065 / Rrim(I) all: 0.11 / Net I/σ(I): 7.4 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 2 %
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1BSY Resolution: 2→13.81 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.902 / SU B: 6.887 / SU ML: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.198 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.79 Å2 / Biso mean: 28.2 Å2 / Biso min: 12.76 Å2
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Refinement step | Cycle: final / Resolution: 2→13.81 Å
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Refine LS restraints |
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