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Yorodumi- PDB-7pnh: X-ray structure of the adduct formed upon reaction of Pt(II) comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pnh | ||||||
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Title | X-ray structure of the adduct formed upon reaction of Pt(II) complex 2c with lysozyme | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / metallodrug / platinum / protein interaction / Pt-protein adduct | ||||||
Function / homology | Function and homology information Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å | ||||||
Authors | Ferraro, G. / Merlino, A. | ||||||
Funding support | 1items
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Citation | Journal: Int J Mol Sci / Year: 2021 Title: Reactions with Proteins of Three Novel Anticancer Platinum(II) Complexes Bearing N-Heterocyclic Ligands. Authors: Sacco, F. / Tarchi, M. / Ferraro, G. / Merlino, A. / Facchetti, G. / Rimoldi, I. / Messori, L. / Massai, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pnh.cif.gz | 75.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pnh.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7pnh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pnh_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7pnh_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7pnh_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 7pnh_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/7pnh ftp://data.pdbj.org/pub/pdb/validation_reports/pn/7pnh | HTTPS FTP |
-Related structure data
Related structure data | 7pniC 193lS 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules AAA
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme |
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-Non-polymers , 6 types, 190 molecules
#2: Chemical | ChemComp-GOL / | ||||||||
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#3: Chemical | ChemComp-NO3 / #4: Chemical | #5: Chemical | ChemComp-DMS / | #6: Chemical | ChemComp-IMD / | #7: Water | ChemComp-HOH / | |
-Details
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: 2 Å3/Da / Density % sol: 38.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 20% ethylene glycol 0.1 M sodium acetate buffer pH 4.0 0.6 M sodium nitrate |
-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 PILATUS3 6M / Detector: PIXEL / Date: Mar 4, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96 Å / Relative weight: 1 |
Reflection | Resolution: 1.22→34.52 Å / Num. obs: 35283 / % possible obs: 100 % / Redundancy: 23.2 % / CC1/2: 1 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.012 / Rrim(I) all: 0.057 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 1.22→1.24 Å / Redundancy: 24.3 % / Rmerge(I) obs: 1.531 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1737 / CC1/2: 0.861 / Rpim(I) all: 0.315 / Rrim(I) all: 1.564 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 193L Resolution: 1.22→34.52 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.559 / SU ML: 0.03 / Cross valid method: FREE R-VALUE / ESU R: 0.041 / ESU R Free: 0.043 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: 20.279 Å2
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Refinement step | Cycle: LAST / Resolution: 1.22→34.52 Å
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Refine LS restraints |
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LS refinement shell |
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