[English] 日本語
![](img/lk-miru.gif)
- PDB-6r73: Structure of IMP-13 metallo-beta-lactamase complexed with hydroly... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6r73 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of IMP-13 metallo-beta-lactamase complexed with hydrolysed meropenem | ||||||||||||
![]() | Beta-lactamase | ||||||||||||
![]() | HYDROLASE / Metallo-Beta-Lactamase / Zinc-binding protein / antibiotic resistance | ||||||||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Softley, C.A. / Zak, K. / Kolonko, M. / Sattler, M. / Popowicz, G. | ||||||||||||
Funding support | ![]() ![]()
| ||||||||||||
![]() | ![]() Title: Structure and Molecular Recognition Mechanism of IMP-13 Metallo-beta-Lactamase. Authors: Softley, C.A. / Zak, K.M. / Bostock, M.J. / Fino, R. / Zhou, R.X. / Kolonko, M. / Mejdi-Nitiu, R. / Meyer, H. / Sattler, M. / Popowicz, G.M. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 100.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 75 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 19.3 KB | Display | |
Data in CIF | ![]() | 26.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6r78C ![]() 6r79C ![]() 6rzrC ![]() 6rzsC ![]() 6s0hC ![]() 1dd6S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 25110.533 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.27 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M Bis-Tris pH 6.5, 25% PEG 3350, cryo-protected with MPD |
-Data collection
Diffraction | Mean temperature: 90 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 9, 2018 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9765 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→58.04 Å / Num. obs: 20856 / % possible obs: 97.01 % / Redundancy: 1.9 % / Biso Wilson estimate: 33.2 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.06752 / Net I/σ(I): 7.62 |
Reflection shell | Resolution: 2.3→2.382 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 1.94 / Num. unique obs: 2130 / CC1/2: 0.84 / % possible all: 99.3 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1DD6 Resolution: 2.3→58.04 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.51
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→58.04 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|