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Yorodumi- PDB-7bf7: Mutant L58F of recombinant bovine beta-lactoglobulin in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bf7 | ||||||
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Title | Mutant L58F of recombinant bovine beta-lactoglobulin in complex with tetracaine | ||||||
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 / Resolution: 2.1 Å | ||||||
Authors | Loch, J.I. / Kaczor, K. / 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 | 7bf7.cif.gz | 75.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bf7.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7bf7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bf7_validation.pdf.gz | 623.6 KB | Display | wwPDB validaton report |
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Full document | 7bf7_full_validation.pdf.gz | 623.8 KB | Display | |
Data in XML | 7bf7_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 7bf7_validation.cif.gz | 11.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/7bf7 ftp://data.pdbj.org/pub/pdb/validation_reports/bf/7bf7 | HTTPS FTP |
-Related structure data
Related structure data | 7bf8C 7bf9C 7bgaC 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
#1: Protein | Mass: 18267.031 Da / Num. of mol.: 1 / Mutation: L1A, I2S, L58F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: LGB / Plasmid: pET-Duet / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Origami B(DE3) / References: UniProt: P02754 |
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#2: Chemical | ChemComp-TE4 / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 2.8 M ammonium sulfate in 0.5 M Tris-HCl pH 8.0 |
-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: Nov 4, 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→13.77 Å / Num. obs: 11130 / % possible obs: 98.8 % / Redundancy: 2.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.041 / Rrim(I) all: 0.074 / Net I/σ(I): 7.9 / Num. measured all: 29028 / Scaling rejects: 15 | |||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BSY Resolution: 2.1→13.769 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.92 / SU B: 12.777 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / ESU R: 0.231 / ESU R Free: 0.196 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: 31.557 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→13.769 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: 15.082 Å / Origin y: 4.7599 Å / Origin z: 33.8706 Å
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Refinement TLS group |
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