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- PDB-5l3i: Re-refinement of 4dd6; cisplatin coordination chemistry determina... -
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Open data
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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 | ||||||||||||
![]() | Lysozyme C | ||||||||||||
![]() | HYDROLASE / 4dd6 re-refinements / platinum coordination geometries / histidine / hen egg white lysozyme | ||||||||||||
Function / homology | ![]() Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Helliwell, J.R. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65.9 KB | Display | ![]() |
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PDB format | ![]() | 48.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.1 KB | Display | ![]() |
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Full document | ![]() | 435.1 KB | Display | |
Data in XML | ![]() | 7.9 KB | Display | |
Data in CIF | ![]() | 10.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5l3hC ![]() 4dd6 S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
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Links
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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) ![]() ![]() |
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-Non-polymers , 6 types, 79 molecules ![](data/chem/img/DMS.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NH3.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NH3.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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: ![]() |
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 |
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Processing
Software | Name: PHENIX / Version: 1.9_1692 / Classification: refinement | |||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() 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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