[English] 日本語
![](img/lk-miru.gif)
- 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 | ||||||
---|---|---|---|---|---|---|---|
Title | 100K X-ray diffraction study of a 6-fold molar excess of a cisplatin/carboplatin mixture binding to HEWL | ||||||
![]() | Lysozyme C | ||||||
![]() | HYDROLASE / cisplatin / carboplatin / histidine / relative toxicity / binding occupancy / X-ray radiation damage / radiation therapy / temperature variation and structure | ||||||
Function / homology | ![]() Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Helliwell, J.R. / Tanley, S.W.M. | ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 42.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 28.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 437.3 KB | Display | |
Data in XML | ![]() | 8.5 KB | Display | |
Data in CIF | ![]() | 11.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4gccC ![]() 4gcdC ![]() 4gceC ![]() 4gcfC ![]() 2w1yS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
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) ![]() ![]() |
---|
-Non-polymers , 5 types, 120 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/CPT.gif)
![](data/chem/img/PT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/CPT.gif)
![](data/chem/img/PT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CL / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PT / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.26 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() |
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 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→55.71 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
|