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Yorodumi- PDB-4qgz: X-ray structure of the adduct formed between hen egg white lysozy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qgz | ||||||
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Title | X-ray structure of the adduct formed between hen egg white lysozyme and trans-dimethylamine methylamine dichlorido platinum(II) | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / Lysozyme fold / O-GLYCOSYL HYDROLASE | ||||||
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: 2.51 Å | ||||||
Authors | Russo Krauss, I. / Merlino, A. | ||||||
Citation | Journal: Inorg.Chem. / Year: 2014 Title: Interactions between Anticancer trans-Platinum Compounds and Proteins: Crystal Structures and ESI-MS Spectra of Two Protein Adducts of trans-(Dimethylamino)(methylamino)dichloridoplatinum(II). Authors: Messori, L. / Marzo, T. / Michelucci, E. / Russo Krauss, I. / Navarro-Ranninger, C. / Quiroga, A.G. / Merlino, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qgz.cif.gz | 35.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qgz.ent.gz | 27.6 KB | Display | PDB format |
PDBx/mmJSON format | 4qgz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qg/4qgz ftp://data.pdbj.org/pub/pdb/validation_reports/qg/4qgz | HTTPS FTP |
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-Related 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
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / References: UniProt: P00698, lysozyme | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.09 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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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 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.51→55.1 Å / Num. all: 4246 / Num. obs: 4246 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→55.1 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.893 / SU B: 11.877 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R Free: 0.341 / 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: 50.894 Å2
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Refinement step | Cycle: LAST / Resolution: 2.51→55.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.505→2.57 Å / Total num. of bins used: 20
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