[English] 日本語
![](img/lk-miru.gif)
- PDB-8eo7: Crystal structure of metagenomic beta-lactamase LRA-5 Y69Q/V166E ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8eo7 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of metagenomic beta-lactamase LRA-5 Y69Q/V166E mutant at 2.15 Angstrom resolution | |||||||||
![]() | beta-lactamase | |||||||||
![]() | ANTIMICROBIAL PROTEIN / beta-lactamase precursor / environmental resistome / soil metagenome / mutant | |||||||||
Function / homology | Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / beta-lactam antibiotic catabolic process / Beta-lactamase/transpeptidase-like / beta-lactamase activity / beta-lactamase / response to antibiotic / beta-lactamase![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Power, P. / D'Amico Gonzalez, G. / Centron, D. / Gutkind, G. / Handelsman, J. / Klinke, S. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Playing beta-Lactamase Evolution: Metagenomic Class A beta-Lactamase LRA-5 is an Inactive Enzyme Capable of Rendering an Active beta-Lactamase by Introduction of Y69Q and V166E Substitutions Authors: D'Amico Gonzalez, G. / Handelsman, J. / Centron, D. / Gutkind, G. / Klinke, S. / Power, P. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 108.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 81.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 444.3 KB | Display | |
Data in XML | ![]() | 19.8 KB | Display | |
Data in CIF | ![]() | 27.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8eo5C ![]() 8eo6C ![]() 1e25S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 30972.346 Da / Num. of mol.: 2 / Mutation: Y100Q, V199E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: pET28a / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.41 Å3/Da / Density % sol: 64 % / Description: long bars |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 10.5 / Details: 1.50 M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 29, 2021 / Details: Horizontally and vertically focusing mirrors |
Radiation | Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→48.58 Å / Num. obs: 46812 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.25 / Rpim(I) all: 0.07 / Rrim(I) all: 0.26 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.15→2.22 Å / Redundancy: 13.9 % / Rmerge(I) obs: 2.721 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4010 / CC1/2: 0.687 / Rpim(I) all: 0.75 / Rrim(I) all: 2.823 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 48 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→40.56 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
LS refinement shell | Resolution: 2.15→2.17 Å
|