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Yorodumi- PDB-5lxw: Atomic resolution X-ray crystal structure of cisplatin bound to h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lxw | ||||||
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Title | Atomic resolution X-ray crystal structure of cisplatin bound to hen egg white lysozyme stored for 5 years on the shelf | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / cisplatin lysozyme chemical equilibrium | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å | ||||||
Authors | Helliwell, J.R. | ||||||
Citation | Journal: Zenodo / Year: 2016 Title: Atomic resolution X-ray crystal structure of cisplatin bound to hen egg white lysozyme stored for 5 years 'on the shelf' Authors: Helliwell, J.R. / Simon, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lxw.cif.gz | 98 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lxw.ent.gz | 75.4 KB | Display | PDB format |
PDBx/mmJSON format | 5lxw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lx/5lxw ftp://data.pdbj.org/pub/pdb/validation_reports/lx/5lxw | HTTPS FTP |
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-Related structure data
Related structure data | 4g4a S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.5281/zenodo.154704 / Data set type: diffraction image data / Details: Raw data |
-Links
-Assembly
Deposited unit |
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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 , 6 types, 120 molecules
#2: Chemical | ChemComp-DMS / | ||||||||
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#3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-NA / | #5: Chemical | #6: Chemical | #7: 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: 2.08 Å3/Da / Density % sol: 40.84 % |
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Crystal grow | Temperature: 295 K / Method: batch mode / pH: 4.7 Details: Hen Egg White Lysozyme (49mg, ie 3.2mM), cisplatin (3mg, ie 10mM), 462.5 microlitres of 0.04 M sodium acetate, 462.5 microlitres of 10% sodium chloride, and with 7.5% DMSO (75 microlitres ie ...Details: Hen Egg White Lysozyme (49mg, ie 3.2mM), cisplatin (3mg, ie 10mM), 462.5 microlitres of 0.04 M sodium acetate, 462.5 microlitres of 10% sodium chloride, and with 7.5% DMSO (75 microlitres ie 1mM), pH 4.7, batch crystallisation method and room temperature (295K). The crystallisation pot was kept for five years. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92819 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 28, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 |
Reflection | Resolution: 1→27.39 Å / Num. obs: 57620 / % possible obs: 88.01 % / Redundancy: 8.1 % / Biso Wilson estimate: 11.9 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.071 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1→1.05 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.869 / Mean I/σ(I) obs: 0.5 / CC1/2: 0.076 / % possible all: 80.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4g4a 4g4a Resolution: 1→27.386 Å / SU ML: 0.14 / SU R Cruickshank DPI: 0.027 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.93 Details: Both Phenix_Refine (Afonine et al 2012) and CCP4 Refmac (Murshudov et al 1997) were used for the model refinement, taking advantage of the advantages of each. COOT (Emsley and Cowtan 2004) ...Details: Both Phenix_Refine (Afonine et al 2012) and CCP4 Refmac (Murshudov et al 1997) were used for the model refinement, taking advantage of the advantages of each. COOT (Emsley and Cowtan 2004) was used to inspect the molecular model and the electron density maps.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→27.386 Å
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Refine LS restraints |
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LS refinement shell |
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