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Yorodumi- PDB-4nsj: Carboplatin binding to HEWL in 2M NH4formate, 0.1M HEPES at pH 7.5 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nsj | ||||||
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Title | Carboplatin binding to HEWL in 2M NH4formate, 0.1M HEPES at pH 7.5 | ||||||
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 / SAD / Resolution: 1.7 Å | ||||||
Authors | Tanley, S.W.M. / Diederichs, K. / Kroon-Batenburg, L.M.J. / Levy, C. / Schreurs, A.M.M. / Helliwell, J.R. | ||||||
Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nsj.cif.gz | 44.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nsj.ent.gz | 30 KB | Display | PDB format |
PDBx/mmJSON format | 4nsj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ns/4nsj ftp://data.pdbj.org/pub/pdb/validation_reports/ns/4nsj | HTTPS FTP |
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-Related structure data
Related structure data | 4lt0C 4lt3C 4nsgC 4nshC 4nsiC 2w1yS 4nsf C: citing same article (ref.) S: Starting model for refinement |
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Similar 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 , 5 types, 84 molecules
#2: Chemical | ChemComp-DMS / #3: Chemical | ChemComp-FMT / #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-QPT / | #6: 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: 1.94 Å3/Da / Density % sol: 36.75 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 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 was mixed with 2 l of resevoir solution 2M NH4formate, 0.1M ...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 was mixed with 2 l of resevoir solution 2M NH4formate, 0.1M HEPES at pH 7.5 , VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-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: Aug 8, 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: 1.7→33.5 Å / Num. all: 13055 / Num. obs: 12367 / % possible obs: 94.7 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 63.5 % / Rmerge(I) obs: 0.212 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 30.1 % / Rmerge(I) obs: 0.942 / Mean I/σ(I) obs: 1.4 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: PDB ENTRY 2W1Y Resolution: 1.7→33.5 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.918 / SU B: 2.934 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2 / ESU R: 0.133 / ESU R Free: 0.136 / 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: 19.237 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→33.5 Å
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