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Yorodumi- PDB-4gcb: 100K X-ray diffraction study of a 6-fold molar excess of a cispla... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gcb | ||||||
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Title | 100K X-ray diffraction study of a 6-fold molar excess of a cisplatin/carboplatin mixture binding to HEWL | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / cisplatin / carboplatin / histidine / relative toxicity / binding occupancy / X-ray radiation damage / radiation therapy / temperature variation and structure | ||||||
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: 1.8 Å | ||||||
Authors | Helliwell, J.R. / Tanley, S.W.M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: The crystal structure analysis of the relative binding of cisplatin and carboplatin in a mixture with histidine in a protein studied at 100 and 300 K with repeated X-ray irradiation. Authors: Helliwell, J.R. / Tanley, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gcb.cif.gz | 42.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gcb.ent.gz | 28.3 KB | Display | PDB format |
PDBx/mmJSON format | 4gcb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gc/4gcb ftp://data.pdbj.org/pub/pdb/validation_reports/gc/4gcb | HTTPS FTP |
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-Related structure data
Related structure data | 4gccC 4gcdC 4gceC 4gcfC 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#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 |
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-Non-polymers , 5 types, 120 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PT / | #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: 1.99 Å3/Da / Density % sol: 38.26 % |
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Crystal grow | Temperature: 277 K / pH: 4.7 Details: 49 mg HEWL (3.2 mM), 3 mg cisplatin (10 mM), 3.7 mg carboplatin (10 mM) in 0.04 M sodium acetate buffer (462.5 uL) + 10% sodium chloride precipitant (462.5 uL) + 1 mM DMSO (75 uL), pH 4.7, ...Details: 49 mg HEWL (3.2 mM), 3 mg cisplatin (10 mM), 3.7 mg carboplatin (10 mM) in 0.04 M sodium acetate buffer (462.5 uL) + 10% sodium chloride precipitant (462.5 uL) + 1 mM DMSO (75 uL), 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: May 23, 2012 / 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→55.71 Å / Num. all: 10718 / Num. obs: 10718 / % possible obs: 100 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 113.6 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 78.8 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 44.2 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 14.3 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2W1Y Resolution: 1.8→55.71 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.314 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2 / ESU R: 0.137 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 11.778 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→55.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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