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- PDB-4nsh: Carboplatin binding to HEWL in 0.2M NH4SO4, 0.1M NaAc in 25% PEG ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4nsh | ||||||
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Title | Carboplatin binding to HEWL in 0.2M NH4SO4, 0.1M NaAc in 25% PEG 4000 at pH 4.6 | ||||||
![]() | Lysozyme C | ||||||
![]() | HYDROLASE | ||||||
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 | ![]() ![]() | ||||||
![]() | Tanley, S.W.M. / Diederichs, K. / Kroon-Batenburg, L.M.J. / Levy, C. / Schreurs, A.M.M. / Helliwell, J.R. | ||||||
![]() | ![]() Title: Carboplatin binding to histidine. Authors: Tanley, S.W. / Diederichs, K. / Kroon-Batenburg, L.M. / Levy, C. / Schreurs, A.M. / Helliwell, J.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 66.1 KB | Display | ![]() |
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PDB format | ![]() | 48.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 470.1 KB | Display | ![]() |
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Full document | ![]() | 471.4 KB | Display | |
Data in XML | ![]() | 8.3 KB | Display | |
Data in CIF | ![]() | 10.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4lt0C ![]() 4lt3C ![]() 4nsgC ![]() 4nsiC ![]() 4nsjC ![]() 2w1yS ![]() 4nsf C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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) ![]() ![]() |
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-Non-polymers , 5 types, 74 molecules ![](data/chem/img/DMS.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/QPT.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/QPT.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.11 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 20mg of HEWL (0.6mM) was dissolved in 1ml distilled water. 1.4mg of carboplatin (1.8mM) was added with 75 l DMSO. 2 l of this mixed with 2 l resevoir soultion 0.2M NH4SO4, 0.1M NaAc in 25% ...Details: 20mg of HEWL (0.6mM) was dissolved in 1ml distilled water. 1.4mg of carboplatin (1.8mM) was added with 75 l DMSO. 2 l of this mixed with 2 l resevoir soultion 0.2M NH4SO4, 0.1M NaAc in 25% PEG 4000 at pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: APEX II CCD / Detector: CCD / Date: Jul 29, 2013 |
Radiation | Monochromator: confocal mirror optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30.71 Å / Num. all: 6965 / Num. obs: 6593 / % possible obs: 94.6 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 20.8 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 2.1→2.13 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 2.2 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2W1Y Resolution: 2.1→30.71 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.905 / SU B: 11.476 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2 / ESU R: 0.301 / ESU R Free: 0.229 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.758 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→30.71 Å
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Refine LS restraints |
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