[English] 日本語
![](img/lk-miru.gif)
- PDB-7r57: Escherichia coli type II Asparaginase N24S mutant in its apo form -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7r57 | ||||||
---|---|---|---|---|---|---|---|
Title | Escherichia coli type II Asparaginase N24S mutant in its apo form | ||||||
![]() | L-asparaginase 2 | ||||||
![]() | ANTITUMOR PROTEIN / 3.5.1.1 / Asparaginase / EcAII / hydrolase | ||||||
Function / homology | ![]() asparagine catabolic process / asparaginase / asparaginase activity / outer membrane-bounded periplasmic space / protein homotetramerization / periplasmic space / protein-containing complex / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Maggi, M. / Scotti, C. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structural Aspects of E. coli Type II Asparaginase in Complex with Its Secondary Product L-Glutamate. Authors: Maggi, M. / Scotti, C. #1: ![]() Title: A protease-resistant Escherichia coli asparaginase with outstanding stability and enhanced anti-leukaemic activity in vitro. Authors: Maggi, M. / Mittelman, S.D. / Parmentier, J.H. / Colombo, G. / Meli, M. / Whitmire, J.M. / Merrell, D.S. / Whitelegge, J. / Scotti, C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 567.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 379.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 450.3 KB | Display | |
Data in XML | ![]() | 53.1 KB | Display | |
Data in CIF | ![]() | 80.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7r5qC ![]() 3ecaS 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 on special symmetry positions |
|
-
Components
#1: Protein | Mass: 35428.660 Da / Num. of mol.: 4 / Mutation: N24S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.93 % / Description: Prism |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8 Details: HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) 100 mM pH 8.0, PEG 8000 5%, ETHYLENE GLYCOL 4% |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2017 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.07252 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.34→48.2 Å / Num. obs: 261282 / % possible obs: 98.5 % / Redundancy: 2.8 % / Biso Wilson estimate: 18.55 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.033 / Rrim(I) all: 0.058 / Net I/σ(I): 10.1 / Num. measured all: 724964 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR |
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3ECA Resolution: 1.4→47.09 Å / SU ML: 0.1514 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.2578 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.06 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→47.09 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|