+Open data
-Basic information
Entry | Database: PDB / ID: 7nqb | ||||||
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Title | X.ray structure of the oxaliplatin/beta-lactoglobulin adduct | ||||||
Components | Beta-lactoglobulin | ||||||
Keywords | TRANSPORT PROTEIN / Beta-lactoglobulin / Oxaliplatin / metal-based drugs / drug delivery / protein-metalation | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | ||||||
Authors | Merlino, A. / Loreto, D. / Ferraro, G. | ||||||
Citation | Journal: Pharmaceuticals / Year: 2022 Title: Protein-Based Delivery Systems for Anticancer Metallodrugs: Structure and Biological Activity of the Oxaliplatin/ beta-Lactoglobulin Adduct. Authors: Monti, D.M. / Loreto, D. / Iacobucci, I. / Ferraro, G. / Pratesi, A. / D'Elia, L. / Monti, M. / Merlino, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7nqb.cif.gz | 79 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nqb.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7nqb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nqb_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7nqb_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7nqb_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 7nqb_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nq/7nqb ftp://data.pdbj.org/pub/pdb/validation_reports/nq/7nqb | HTTPS FTP |
-Related structure data
Related structure data | 6zsrS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18301.174 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P02754 #2: Chemical | ChemComp-PT / | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M KCl, 0.04M HEPES, 35% v/v pentaerythritol propoxylate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.96 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→56.3 Å / Num. obs: 17918 / % possible obs: 86.9 % / Redundancy: 2.3 % / Biso Wilson estimate: 19.3 Å2 / CC1/2: 0.958 / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.01→56.3 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 2486 / CC1/2: 0.939 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ZSR Resolution: 2.01→56.3 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.879 / SU B: 6.658 / SU ML: 0.182 / Cross valid method: FREE R-VALUE / ESU R: 0.281 / ESU R Free: 0.231 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: 24.961 Å2
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Refinement step | Cycle: LAST / Resolution: 2.01→56.3 Å
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Refine LS restraints |
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LS refinement shell |
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