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Yorodumi- PDB-5l3i: Re-refinement of 4dd6; cisplatin coordination chemistry determina... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5l3i | ||||||||||||
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Title | Re-refinement of 4dd6; cisplatin coordination chemistry determination at hen egg white lysozyme His15 | ||||||||||||
Components | Lysozyme C | ||||||||||||
Keywords | HYDROLASE / 4dd6 re-refinements / platinum coordination geometries / histidine / hen egg white lysozyme | ||||||||||||
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: 1.7 Å | ||||||||||||
Authors | Helliwell, J.R. | ||||||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: ArXiv / Year: 2016 Title: Cisplatin coordination chemistry determination at hen egg white lysozyme His15 with ligand distances and angles, and their standard uncertainties, and also reporting a split occupancy effect Authors: Helliwell, J.R. / Schreurs, A.M.M. / Kroon-Batenburg, L.M.J. / Tanley, S. #1: Journal: ArXiv / Year: 2016 Title: Cisplatin coordination chemistry determination at hen egg white lysozyme His15 with ligand distances and angles, and their standard uncertainties, and also reporting a split occupancy effect Authors: Helliwell, J.R. / Tanley, S. / Schreurs, A.M.M. / Kroon-Batenburg, L.M.J. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l3i.cif.gz | 65.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l3i.ent.gz | 48.2 KB | Display | PDB format |
PDBx/mmJSON format | 5l3i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l3/5l3i ftp://data.pdbj.org/pub/pdb/validation_reports/l3/5l3i | HTTPS FTP |
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-Related structure data
Related structure data | 5l3hC 4dd6 S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.15127/1.219236 / Data set type: diffraction image 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) / Plasmid details: hen egg white / References: UniProt: P00698, lysozyme |
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-Non-polymers , 6 types, 79 molecules
#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-PT / #5: Chemical | ChemComp-CL / #6: Chemical | #7: 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: 1.97 Å3/Da / Density % sol: 37.5 % |
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Crystal grow | Temperature: 295 K / Method: batch mode / pH: 4.7 Details: HEWL CO-CRYSTALLIZED WITH CISPLATIN IN 462.5 microL 0.05 M SODIUM ACETATE AND 462.5 microL 10% SODIUM CHLORIDE IN 75 microL DMSO, PH 4.7, BATCH, TEMPERATURE 295K. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Nov 25, 2010 / Details: CONFOCAL MIRROR OPTICS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→18.39 Å / Num. obs: 10869 / % possible obs: 83.05 % / Redundancy: 25 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 35.1 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 18 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 8.1 / % possible all: 100 |
-Processing
Software | Name: PHENIX / Version: 1.9_1692 / Classification: refinement | |||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4dd6 4dd6 Resolution: 1.7→18.389 Å / SU ML: 0.14 / SU R Cruickshank DPI: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.15
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→18.389 Å
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Refine LS restraints |
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LS refinement shell |
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