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Yorodumi- PDB-4z3m: X-ray structure of the adduct formed in the reaction between lyso... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4z3m | ||||||
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Title | X-ray structure of the adduct formed in the reaction between lysozyme and a platinum(II) Complex with S,O Bidentate Ligands (9b) | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / Pt compounds / anticancer agents / lysozyme complexes | ||||||
Function / homology | Function and homology information Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / 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 / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Merlino, A. | ||||||
Citation | Journal: Inorg.Chem. / Year: 2015 Title: Platinum(II) Complexes with O,S Bidentate Ligands: Biophysical Characterization, Antiproliferative Activity, and Crystallographic Evidence of Protein Binding. Authors: Mugge, C. / Marzo, T. / Massai, L. / Hildebrandt, J. / Ferraro, G. / Rivera-Fuentes, P. / Metzler-Nolte, N. / Merlino, A. / Messori, L. / Weigand, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4z3m.cif.gz | 44.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z3m.ent.gz | 29.9 KB | Display | PDB format |
PDBx/mmJSON format | 4z3m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/4z3m ftp://data.pdbj.org/pub/pdb/validation_reports/z3/4z3m | HTTPS FTP |
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-Related structure data
Related structure data | 4z41C 4j4tS 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 A
#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 , 5 types, 109 molecules
#2: Chemical | ChemComp-4KV / | ||||
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#3: Chemical | ChemComp-DMS / | ||||
#4: Chemical | #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.57 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 20% ethylene glycol, 0.1 M sodium acetate pH 4.5, 0.6 M sodium nitrate PH range: 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: No cryoprotectant was used |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 17, 2014 |
Radiation | Monochromator: filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→55.34 Å / Num. all: 43330 / Num. obs: 6498 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.15→2.2 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.9 / % possible all: 99.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4j4t Resolution: 2.15→55.34 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.549 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.31 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.707 Å2
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Refinement step | Cycle: 1 / Resolution: 2.15→55.34 Å
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Refine LS restraints |
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