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Yorodumi- PDB-7bga: Mutant F105A of recombinant beta-lactoglobulin in complex with en... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bga | ||||||
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Title | Mutant F105A of recombinant beta-lactoglobulin in complex with endogenous ligand | ||||||
Components | Beta-lactoglobulin | ||||||
Keywords | TRANSPORT PROTEIN / lactoglobulin / mutant / ligand | ||||||
Function / homology | Function and homology information retinol binding / long-chain fatty acid binding / extracellular space / identical protein binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Loch, J.I. / Lazinska, I. / Lewinski, K. | ||||||
Funding support | Poland, 1items
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Citation | Journal: Acta Biochim.Pol. / Year: 2021 Title: Interactions of new lactoglobulin variants with tetracaine: crystallographic studies of ligand binding to lactoglobulin mutants possessing single substitution in the binding pocket. Authors: Loch, J. / Bonarek, P. / Siuda, M. / Wrobel, P. / Lewinski, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bga.cif.gz | 75.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bga.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7bga.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bga_validation.pdf.gz | 448.4 KB | Display | wwPDB validaton report |
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Full document | 7bga_full_validation.pdf.gz | 448.9 KB | Display | |
Data in XML | 7bga_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 7bga_validation.cif.gz | 12.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/7bga ftp://data.pdbj.org/pub/pdb/validation_reports/bg/7bga | HTTPS FTP |
-Related structure data
Related structure data | 7bf7C 7bf8C 7bf9C 7bgxC 7bgzC 7bh0C 1bsyS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 18156.918 Da / Num. of mol.: 1 / Mutation: L1A, I2S, F105A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: LGB / Plasmid: pET-Duet-1 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Origami B(DE3) / References: UniProt: P02754 |
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#2: Chemical | ChemComp-DAO / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 2.6 M ammonium sulfate in 0.5 M Tris-HCl pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 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 9, 2015 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→15.4 Å / Num. obs: 15168 / % possible obs: 99.7 % / Redundancy: 2.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.045 / Rrim(I) all: 0.081 / Net I/σ(I): 12 / Num. measured all: 40802 / Scaling rejects: 25 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1bsy Resolution: 1.9→13.789 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.126 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.145 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.742 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→13.789 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 15.1697 Å / Origin y: 4.5671 Å / Origin z: 33.6043 Å
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Refinement TLS group |
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