[English] 日本語
![](img/lk-miru.gif)
- PDB-4gzb: Crystal structure of native AmpC beta-lactamase from Pseudomonas ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4gzb | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of native AmpC beta-lactamase from Pseudomonas aeruginosa PAO1 | ||||||
![]() | Beta-lactamase![]() | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() antibiotic catabolic process / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Benvenuti, M. / De Luca, F. / Docquier, J.D. / Mangani, S. | ||||||
![]() | ![]() Title: Structural insight into potent broad-spectrum inhibition with reversible recyclization mechanism: avibactam in complex with CTX-M-15 and Pseudomonas aeruginosa AmpC beta-lactamases Authors: Lahiri, S.D. / Mangani, S. / Durand-Reville, T. / Benvenuti, M. / De Luca, F. / Sanyal, G. / Docquier, J.D. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 156.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 124.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 4hbtC ![]() 4hbuC ![]() 4hefC ![]() 1ke4S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | ![]() Mass: 40723.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-EDO / ![]() |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.91 % |
---|---|
Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1M Tris, 20% PEG 8000, O.1M K2HPO4, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2009 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.79→46.617 Å / Num. all: 38317 / Num. obs: 38317 / % possible obs: 83.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 26.695 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 1.79→1.89 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 1.8 / Num. unique all: 9784 / % possible all: 82.7 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1KE4 Resolution: 1.79→34.51 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.065 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.534 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.132 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.79→34.51 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.79→1.836 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -35.2493 Å / Origin y: 12.2298 Å / Origin z: -14.3113 Å
|