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Yorodumi- PDB-4owb: Cisplatin binding to HEWL under sodium bromide crystallisation co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4owb | ||||||
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Title | Cisplatin binding to HEWL under sodium bromide crystallisation conditions | ||||||
Components | Lysozyme C | ||||||
Keywords | 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 / Resolution: 1.69 Å | ||||||
Authors | Tanley, S.W.M. / Helliwell, J.R. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2014 Title: Chemical conversion of cisplatin and carboplatin with histidine in a model protein crystallized under sodium iodide conditions. Authors: Tanley, S.W. / Helliwell, J.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4owb.cif.gz | 43.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4owb.ent.gz | 28.6 KB | Display | PDB format |
PDBx/mmJSON format | 4owb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/4owb ftp://data.pdbj.org/pub/pdb/validation_reports/ow/4owb | 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
-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 , 8 types, 120 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-MEB / | #6: Chemical | ChemComp-BR / #7: Chemical | #8: Chemical | ChemComp-CL / | #9: Water | ChemComp-HOH / | |
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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: 1.99 Å3/Da / Density % sol: 38.32 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 4.7 Details: 20mg HEWL co-crystallised with 1.2mg cisplatin with 75?l DMSO, 462.5?l 0.1M NaAc and 462.5?l 1M NaBr solution |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å |
Detector | Type: APEX II CCD / Detector: CCD / Date: Nov 26, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→30.99 Å / Num. obs: 24594 / % possible obs: 99.8 % / Redundancy: 55.1 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 29.7 |
Reflection shell | Resolution: 1.694→1.79 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.661 / Mean I/σ(I) obs: 1.5 / % possible all: 98.7 |
-Processing
Software | Name: REFMAC / Version: 5.8.0049 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.69→30.99 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.887 / SU B: 3.097 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.603 Å2
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Refinement step | Cycle: 1 / Resolution: 1.69→30.99 Å
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