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- PDB-6zsr: Crystal structure of the Cisplatin beta-Lactoglobulin adduct form... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zsr | ||||||
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Title | Crystal structure of the Cisplatin beta-Lactoglobulin adduct formed after 72 h of soaking | ||||||
![]() | Beta-lactoglobulin![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Balasco, N. / Ferraro, G. / Merlino, A. | ||||||
![]() | ![]() Title: Cisplatin binding to beta-lactoglobulin: a structural study. Authors: Balasco, N. / Ferraro, G. / Loreto, D. / Iacobucci, I. / Monti, M. / Merlino, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.2 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6zsqC ![]() 1bebS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain: (Details: Chains AAA BBB) |
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Components
#1: Protein | ![]() Mass: 18301.174 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #2: Chemical | ![]() #3: Chemical | ChemComp-PT / #4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.59 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: Crystals of beta-Lactoglobulin were grown using 3.0 M (NH4)2SO4, 0.1 M sodium/potassium phosphate buffer pH 6.9 as reservoir. Protein crystallizes at a concentration of 18 mg/mL. Crystals of ...Details: Crystals of beta-Lactoglobulin were grown using 3.0 M (NH4)2SO4, 0.1 M sodium/potassium phosphate buffer pH 6.9 as reservoir. Protein crystallizes at a concentration of 18 mg/mL. Crystals of beta-Lactoglobulin were soaked in a solution consisting of 3.0 M (NH4)2SO4, 0.1 M sodium/potassium phosphate buffer (pH 6.9) with 5 mM CDDP (about 1:3 protein to metal ratio). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2→43.91 Å / Num. obs: 17566 / % possible obs: 86 % / Redundancy: 3.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.077 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2→2.06 Å / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1251 / CC1/2: 0.89 / % possible all: 83.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1BEB Resolution: 2.005→23.295 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.893 / WRfactor Rfree: 0.29 / WRfactor Rwork: 0.201 / SU B: 6.448 / SU ML: 0.181 / Average fsc free: 0.8532 / Average fsc work: 0.8932 / Cross valid method: FREE R-VALUE / ESU R: 0.387 / ESU R Free: 0.274 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: 22.458 Å2
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Refinement step | Cycle: LAST / Resolution: 2.005→23.295 Å
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Refine LS restraints |
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LS refinement shell |
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