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Yorodumi- PDB-7zcd: Mutant L39Y-L58F of recombinant bovine beta-lactoglobulin in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zcd | ||||||
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Title | Mutant L39Y-L58F of recombinant bovine beta-lactoglobulin in complex with pramocaine | ||||||
Components | Beta-lactoglobulin | ||||||
Keywords | TRANSPORT PROTEIN / lactoglobulin / mutation / 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. / Kurpiewska, K. / Bonarek, P. | ||||||
Funding support | 1items
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Citation | Journal: J.Mol.Recognit. / Year: 2023 Title: beta-Lactoglobulin variants as potential carriers of pramoxine: Comprehensive structural and biophysical studies. Authors: Bonarek, P. / Mularczyk, D. / Loch, J.I. / Kurpiewska, K. / Dziedzicka-Wasylewska, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zcd.cif.gz | 75.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zcd.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7zcd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zcd_validation.pdf.gz | 612.7 KB | Display | wwPDB validaton report |
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Full document | 7zcd_full_validation.pdf.gz | 613.4 KB | Display | |
Data in XML | 7zcd_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 7zcd_validation.cif.gz | 11 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/7zcd ftp://data.pdbj.org/pub/pdb/validation_reports/zc/7zcd | HTTPS FTP |
-Related structure data
Related structure data | 7z9zC 7za0C 7zlfC 1bsyS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 18317.047 Da / Num. of mol.: 1 / Mutation: L1A, I2S, L39Y, L58F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: LGB / Plasmid: pET-Duet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P02754 |
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#2: Chemical | ChemComp-PX9 / |
#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: 2.51 Å3/Da / Density % sol: 50.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 2.2M ammonium sulfate, 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: 1.54056 Å |
Detector | Type: AGILENT ATLAS CCD / Detector: CCD / Date: Oct 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54056 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→14.99 Å / Num. obs: 11262 / % possible obs: 99.6 % / Redundancy: 6.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.091 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.1→2.16 Å / Rmerge(I) obs: 1.373 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 919 / CC1/2: 0.654 / Rrim(I) all: 1.551 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BSY Resolution: 2.1→14.99 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / SU B: 15.246 / SU ML: 0.185 / Cross valid method: FREE R-VALUE / ESU R: 0.248 / ESU R Free: 0.209
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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: 45.685 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→14.99 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: -15.5529 Å / Origin y: 4.5825 Å / Origin z: 3.5356 Å
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Refinement TLS group | Selection: ALL |