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Yorodumi- PDB-5io6: Bovine beta-lactoglobulin complex with dodecane, ambient pressure -
+Open data
-Basic information
Entry | Database: PDB / ID: 5io6 | ||||||
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Title | Bovine beta-lactoglobulin complex with dodecane, ambient pressure | ||||||
Components | Major allergen beta-lactoglobulin | ||||||
Keywords | TRANSPORT PROTEIN / BETA-LACTOGLOBULIN / LIPOCALIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.851 Å | ||||||
Authors | Kurpiewska, K. / Biela, A. | ||||||
Funding support | Poland, 1items
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Citation | Journal: Colloids Surf B Biointerfaces / Year: 2017 Title: Investigation of high pressure effect on the structure and adsorption of beta-lactoglobulin. Authors: Kurpiewska, K. / Biela, A. / Loch, J.I. / Swiatek, S. / Jachimska, B. / Lewinski, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5io6.cif.gz | 47.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5io6.ent.gz | 32 KB | Display | PDB format |
PDBx/mmJSON format | 5io6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/io/5io6 ftp://data.pdbj.org/pub/pdb/validation_reports/io/5io6 | HTTPS FTP |
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-Related structure data
Related structure data | 5io5C 5io7C 3lbgS C: citing same article (ref.) S: Starting model for refinement |
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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: 18387.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: MILK / References: UniProt: B5B0D4 |
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#2: Chemical | ChemComp-D12 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.34 M citric sodium |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 0.71069 Å |
Detector | Type: Nonius Kappa CCD / Detector: CCD / Date: Nov 26, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.71069 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→20.15 Å / Num. obs: 4645 / % possible obs: 96 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 1.6 |
Reflection shell | Resolution: 2.85→3.04 Å / Rmerge(I) obs: 0.495 / Net I/σ(I) obs: 4.22 / % possible all: 97.4 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LBG Resolution: 2.851→20.15 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.69
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.46 Å2 / Biso mean: 20.8654 Å2 / Biso min: 0.19 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.851→20.15 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3
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