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- PDB-5k06: Recombinant bovine beta-lactoglobulin with uncleaved N-terminal m... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5k06 | ||||||
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Title | Recombinant bovine beta-lactoglobulin with uncleaved N-terminal methionine (rBlgB) | ||||||
![]() | Beta-lactoglobulin | ||||||
![]() | TRANSPORT PROTEIN / lipocalin | ||||||
Function / homology | ![]() retinol binding / long-chain fatty acid binding / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Loch, J.I. / Bonarek, P. / Tworzydlo, M. / Polit, A. / Hawro, B. / Lach, A. / Ludwin, E. / Lewinski, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Engineered beta-Lactoglobulin Produced in E. coli: Purification, Biophysical and Structural Characterisation. Authors: Loch, J.I. / Bonarek, P. / Tworzydo, M. / Polit, A. / Hawro, B. / Lach, A. / Ludwin, E. / 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 | ![]() | 49.6 KB | Display | ![]() |
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PDB format | ![]() | 34.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5htdC ![]() 5hteC ![]() 1bebS 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: 18432.369 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: additional N-terminal residue - uncleaved start Met (Met0) Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-MYR / |
#4: Chemical | ChemComp-SIN / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 3.0 M (NH4)2SO4 solution in 0.2 M Tris-HCl buffer, pH from 7.8 to 8.8 PH range: 7.8 to 8.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 25, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→9.98 Å / Num. obs: 7101 / % possible obs: 99.6 % / Redundancy: 19.7 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 64.7 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 20.4 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 16.1 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1BEB Resolution: 2.5→9.98 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.84 / SU B: 11.937 / SU ML: 0.273 / Cross valid method: THROUGHOUT / ESU R: 0.883 / ESU R Free: 0.41 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.303 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→9.98 Å
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Refine LS restraints |
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