[English] 日本語
Yorodumi- PDB-6zsq: Crystal structure of the Cisplatin beta-Lactoglobulin adduct form... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zsq | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the Cisplatin beta-Lactoglobulin adduct formed after 18 h of soaking | ||||||
Components | Beta-lactoglobulin | ||||||
Keywords | TRANSPORT PROTEIN / Complex / Drug delivery system / Cisplatin | ||||||
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: 2.004 Å | ||||||
Authors | Balasco, N. / Ferraro, G. / Merlino, A. | ||||||
Citation | Journal: Dalton Trans / Year: 2020 Title: Cisplatin binding to beta-lactoglobulin: a structural study. Authors: Balasco, N. / Ferraro, G. / Loreto, D. / Iacobucci, I. / Monti, M. / Merlino, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6zsq.cif.gz | 84 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6zsq.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6zsq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/6zsq ftp://data.pdbj.org/pub/pdb/validation_reports/zs/6zsq | HTTPS FTP |
---|
-Related structure data
Related structure data | 6zsrC 1bebS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18329.229 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P02754 #2: Chemical | ChemComp-NH3 / | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.12 % |
---|---|
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 |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 16, 2018 |
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→23.23 Å / Num. obs: 17918 / % possible obs: 86.9 % / Redundancy: 2.3 % / CC1/2: 0.958 / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2→2.06 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 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BEB Resolution: 2.004→23.228 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.195 / SU ML: 0.141 / Cross valid method: FREE R-VALUE / ESU R: 0.265 / ESU R Free: 0.193 Details: Hydrogens have been added in their riding positions
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 22.264 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.004→23.228 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|