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Yorodumi- PDB-4yen: Room temperature X-ray diffraction studies of cisplatin binding t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yen | ||||||
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Title | Room temperature X-ray diffraction studies of cisplatin binding to HEWL in DMSO media after 14 months of crystal storage - new refinement | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / Re-refinement of 4G4A / Cisplatin / Metal binding | ||||||
Function / homology | Function and homology information Lactose synthesis / 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 ...Lactose synthesis / 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 / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Shabalin, I.G. / Dauter, Z. / Jaskolski, M. / Minor, W. / Wlodawer, A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin. Authors: Shabalin, I. / Dauter, Z. / Jaskolski, M. / Minor, W. / Wlodawer, A. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2012 Title: Room-temperature X-ray diffraction studies of cisplatin and carboplatin binding to His15 of HEWL after prolonged chemical exposure. Authors: Tanley, S.W. / Schreurs, A.M. / Kroon-Batenburg, L.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 | 4yen.cif.gz | 69.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yen.ent.gz | 49.1 KB | Display | PDB format |
PDBx/mmJSON format | 4yen.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/4yen ftp://data.pdbj.org/pub/pdb/validation_reports/ye/4yen | HTTPS FTP |
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-Related structure data
Related structure data | 4ydxC 4yeaC 4yemC 4yeoC 4g4a S: Starting model for refinement C: citing same article (ref.) |
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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
#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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#2: Chemical | #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-DMS / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.68 % |
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Crystal grow | Temperature: 295 K / Method: batch mode / pH: 4.7 Details: HEWL co-crystallized with cisplatin with 5% DMSO media in 1 mL 10% sodium chloride + 1 ml 0.04 M sodium acetate, pH 4.7 |
-Data collection
Diffraction | Mean temperature: 295 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: APEX II CCD / Detector: CCD / Date: Jan 25, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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→50 Å / Num. all: 8602 / Num. obs: 8602 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.032 / Rrim(I) all: 0.092 / Rsym value: 0.086 / Χ2: 0.905 / Net I/av σ(I): 19.439 / Net I/σ(I): 8.8 / Num. measured all: 68208 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4G4A 4g4a Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.1507 / WRfactor Rwork: 0.1277 / FOM work R set: 0.884 / SU B: 6.737 / SU ML: 0.093 / SU R Cruickshank DPI: 0.161 / SU Rfree: 0.1334 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS This deposit resulted from an analysis of a number of PDB entries that contain cisplatin or carboplatin in complex ...Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS This deposit resulted from an analysis of a number of PDB entries that contain cisplatin or carboplatin in complex with proteins, conducted in the spirit of the Terwilliger-Bricogne motto advocating continuous improvement of the macromolecular models in the PDB (Acta Cryst. D70, 2533, 2014). Since the original data frames for this structure are available at the http://rawdata.chem.uu.nl server, they have been re-processed, and the new structure factors have been used for the present re-refinement. The coordinates originally deposited as 4G4A were used as the starting point for this independent re-refinement. The new model is based on data extending to higher resolution, includes some reinterpretation of the ligands, has lower R factors, and improved statistics describing the agreement with the experimental data.
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.67 Å2 / Biso mean: 28.046 Å2 / Biso min: 10.87 Å2
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Refinement step | Cycle: final / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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