[English] 日本語
![](img/lk-miru.gif)
- PDB-9bzq: Structure of Class A Beta-lactamase from Bordetella bronchiseptic... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 9bzq | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Class A Beta-lactamase from Bordetella bronchiseptica RB50 in a complex with Avibactam | ||||||
![]() | class A Beta-lactamase, PenP superfamily | ||||||
![]() | HYDROLASE / lactamase / serine hydrolase / PenP / CSBID / Center for Structural Biology of Infectious Diseases / Avibactam | ||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Maltseva, N. / Kim, Y. / Endres, M. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID) | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structure of Class A Beta-lactamase from Bordetella bronchiseptica RB50 in a complex with Avibactam Authors: Maltseva, N. / Kim, Y. / Endres, M. / Joachimiak, A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 147.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 92.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 778 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 778.2 KB | Display | |
Data in XML | ![]() | 14.8 KB | Display | |
Data in CIF | ![]() | 22.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 28914.463 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: BB2049 / Plasmid: p53 / Production host: ![]() ![]() |
---|
-Non-polymers , 5 types, 311 molecules ![](data/chem/img/NXL.gif)
![](data/chem/img/SIN.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SIN.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NXL / ( |
---|---|
#3: Chemical | ChemComp-SIN / |
#4: Chemical | ChemComp-FMT / |
#5: Chemical | ChemComp-EDO / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.61 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Succinic acid pH 7.0; 15% (v/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→50 Å / Num. obs: 39292 / % possible obs: 99.8 % / Redundancy: 4.9 % / Biso Wilson estimate: 7.6 Å2 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.016 / Net I/σ(I): 48.8 |
Reflection shell | Resolution: 1.47→1.5 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.079 / Num. unique obs: 1936 / CC1/2: 0.992 / Rpim(I) all: 0.04 / % possible all: 98.4 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.19 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.47→26.01 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|