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- PDB-6rwr: Engineered beta-lactoglobulin: variant M107L in complex with myri... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6rwr | ||||||
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Title | Engineered beta-lactoglobulin: variant M107L in complex with myristic acid | ||||||
![]() | Beta-lactoglobulin | ||||||
![]() | TRANSPORT PROTEIN / lipocalin / mutation | ||||||
Function / homology | ![]() retinol binding / long-chain fatty acid binding / extracellular space / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Loch, J.I. / Gotkowski, M. / Lewinski, 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 | ![]() | 80.2 KB | Display | ![]() |
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PDB format | ![]() | 59.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 590.9 KB | Display | ![]() |
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Full document | ![]() | 591.1 KB | Display | |
Data in XML | ![]() | 9.1 KB | Display | |
Data in CIF | ![]() | 11.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6qi6C ![]() 6qi7C ![]() 6qpdC ![]() 6qpeC ![]() 6rwpC ![]() 6rwqC ![]() 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 18214.977 Da / Num. of mol.: 1 / Mutation: L1A, I2S, M107L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MYR / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.34 M tri-sodium citrate, 0.1 M Tris 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: 1.54 Å | ||||||||||||||||||||||||||||||
Detector | Type: AGILENT ATLAS CCD / Detector: CCD / Date: Dec 18, 2014 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→14.2 Å / Num. obs: 11138 / % possible obs: 99.1 % / Redundancy: 2.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.041 / Rrim(I) all: 0.071 / Net I/σ(I): 10.9 / Num. measured all: 29317 / Scaling rejects: 7 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1BSY Resolution: 2.1→13.47 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.933 / SU B: 9.663 / SU ML: 0.127 / SU R Cruickshank DPI: 0.2031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.177 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 115.12 Å2 / Biso mean: 35.314 Å2 / Biso min: 13.39 Å2
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Refinement step | Cycle: final / Resolution: 2.1→13.47 Å
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Refine LS restraints |
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