+Open data
-Basic information
Entry | Database: PDB / ID: 4ddb | ||||||
---|---|---|---|---|---|---|---|
Title | EVAL processed HEWL, cisplatin DMSO paratone pH 6.5 | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / hen egg white lysozyme (HEWL) / platinum / N-acetylglucosamine | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 3 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4ddb.cif.gz | 65.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4ddb.ent.gz | 48.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ddb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/4ddb ftp://data.pdbj.org/pub/pdb/validation_reports/dd/4ddb | HTTPS FTP |
---|
-Related structure data
Related structure data | 4dd0C 4dd1C 4dd2C 4dd3C 4dd7C 4dd9C 4ddaC 4ddcC 2w1yS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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) Gallus gallus (chicken) / Tissue: egg white / References: UniProt: P00698, lysozyme | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-DMS / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.94 % |
---|---|
Crystal grow | Temperature: 277 K / Method: batch / pH: 6.5 Details: HEWL co-crystallized with cisplatin in 462.5 uL 0.05 M sodium acetate, pH 6.5, 462.5 uL 10% sodium chloride, and 75 uL DMSO, BATCH, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 9, 2011 / Details: Osmic Confocal Max-Flux, blue configuration |
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: 2.5→30.94 Å / Num. all: 3234 / Num. obs: 1772 / % possible obs: 54.7 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 24.6 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 2.5→2.58 Å / Redundancy: 24.5 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 6.1 / % possible all: 97.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2W1Y Resolution: 3→28.16 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.842 / SU B: 48.053 / SU ML: 0.499 / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2 / ESU R Free: 0.748 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 17.811 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→28.16 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3→3.077 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -0.2933 Å / Origin y: -20.8895 Å / Origin z: 8.9398 Å
|