+Open data
-Basic information
Entry | Database: PDB / ID: 4ddc | ||||||
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Title | EVAL processed HEWL, cisplatin DMSO NAG silicone oil | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / hen egg white lysozyme (HEWL) / platinum / N-acetylglucosamine | ||||||
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: 1.8 Å | ||||||
Authors | Tanley, S.W. / Schreurs, A.M. / Kroon-Batenburg, L.M. / Meredith, J. / Prendergast, R. / Walsh, D. / Bryant, P. / Levy, C. / Helliwell, J.R. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Structural studies of the effect that dimethyl sulfoxide (DMSO) has on cisplatin and carboplatin binding to histidine in a protein. Authors: Tanley, S.W. / Schreurs, A.M. / Kroon-Batenburg, L.M. / Meredith, J. / Prendergast, R. / Walsh, D. / Bryant, P. / Levy, C. / 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 | 4ddc.cif.gz | 66.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ddc.ent.gz | 48.5 KB | Display | PDB format |
PDBx/mmJSON format | 4ddc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/4ddc ftp://data.pdbj.org/pub/pdb/validation_reports/dd/4ddc | HTTPS FTP |
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-Related structure data
Related structure data | 4dd0C 4dd1C 4dd2C 4dd3C 4dd7C 4dd9C 4ddaC 4ddbC 2w1yS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 1 - 129 / Label seq-ID: 1 - 129
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-Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 2 / Fragment: UNP residues 19-147 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: egg white / References: UniProt: P00698, lysozyme #2: Chemical | ChemComp-CPT / #3: Chemical | ChemComp-DMS / #4: 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: 1.99 Å3/Da / Density % sol: 38.15 % |
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Crystal grow | Temperature: 277 K / Method: batch / pH: 4.7 Details: HEWL co-crystallized with cisplatin and N-acetylglucosamine in 462.5 uL 0.05 M sodium acetate and 462.5 uL 10% sodium chloride in 75 uL DMSO, pH 4.7, BATCH, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Jul 25, 2011 / Details: Incoatec Helios confocal optics |
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: 1.8→79.089 Å / Num. all: 21949 / Num. obs: 21843 / % possible obs: 94.6 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 15.1 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 4.2 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2W1Y Resolution: 1.8→19.17 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.897 / SU B: 2.981 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.15 / 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: 16.387 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.17 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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