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- PDB-4lt3: HEWL co-crystallized with Carboplatin in non-NaCl conditions: cry... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4lt3 | ||||||
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Title | HEWL co-crystallized with Carboplatin in non-NaCl conditions: crystal 2 processed using the XDS software package | ||||||
![]() | Lysozyme C | ||||||
![]() | HYDROLASE / histidine / MPD / avoid partial conversion to cisplatin / pair-wise refinement technique / DPI / resolution limit choice / glycosyl 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. / 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 | ![]() | 41.6 KB | Display | ![]() |
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PDB format | ![]() | 28 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 761 KB | Display | ![]() |
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Full document | ![]() | 761.5 KB | Display | |
Data in XML | ![]() | 8.2 KB | Display | |
Data in CIF | ![]() | 10.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4lt0C ![]() 4nsgC ![]() 4nshC ![]() 4nsiC ![]() 4nsjC ![]() 2w1yS 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
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Fragment: UNP residues 19-147 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-DMS / #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.15 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 2 uL protein/carboplatin/DMSO solution [20 mg (0.6 mM) HEWL + 1.4 mg (1.8 mM) carboplatin in 1 mL distilled water + 75 uL DMSO] + 2 uL reservoir solution [65% MPD, 0.1 M citric acid, pH 4.0] ...Details: 2 uL protein/carboplatin/DMSO solution [20 mg (0.6 mM) HEWL + 1.4 mg (1.8 mM) carboplatin in 1 mL distilled water + 75 uL DMSO] + 2 uL reservoir solution [65% MPD, 0.1 M citric acid, pH 4.0] against 1 mL of reservoir solution, crystals grew after ~4 weeks, data collected 5 weeks after crystal growth, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 127 K |
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Diffraction source | Source: ![]() |
Detector | Type: APEX II CCD / Detector: CCD / Date: May 8, 2013 |
Radiation | Monochromator: tunable graphite crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→39.41 Å / Num. all: 7850 / Num. obs: 7488 / % possible obs: 95 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 0.5 / Rmerge(I) obs: 0.248 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2→2.05 Å / Rmerge(I) obs: 2.27 / Mean I/σ(I) obs: 0.5 / % possible all: 32.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2W1Y Resolution: 2→27.28 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.903 / SU B: 5.823 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 4 / ESU R: 0.234 / ESU R Free: 0.2 / 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: 27.677 Å2
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Refinement step | Cycle: LAST / Resolution: 2→27.28 Å
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Refine LS restraints |
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