[English] 日本語
![](img/lk-miru.gif)
- PDB-2aaf: Structure of H278A arginine deiminase with L-arginine forming a S... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2aaf | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of H278A arginine deiminase with L-arginine forming a S-alkylthiouronium reaction intermediate | ||||||
![]() | Arginine deiminase | ||||||
![]() | HYDROLASE / arginine degradation pathway / L-arginine deiminase / catalytic mechanism | ||||||
Function / homology | ![]() arginine deiminase / arginine deiminase activity / arginine deiminase pathway / arginine catabolic process to ornithine / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Galkin, A. / Lu, X. / Dunaway-Mariano, D. / Herzberg, O. | ||||||
![]() | ![]() Title: Crystal Structures Representing the Michaelis Complex and the Thiouronium Reaction Intermediate of Pseudomonas aeruginosa Arginine Deiminase. Authors: Galkin, A. / Lu, X. / Dunaway-Mariano, D. / Herzberg, O. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 337 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 276.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 2a9gSC ![]() 2abrC ![]() 2aciC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a tetramer generated from the molecules A, B, C and D in the asymmetric unit |
-
Components
#1: Protein | Mass: 46582.000 Da / Num. of mol.: 4 / Mutation: H278A 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: 2.24 Å3/Da / Density % sol: 45 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 34% MPD (2-methyl-2,4-pentanediol), 6% PEG 3350, 0.1 M Tris-HCl (pH 7.6), L-arginine 0.02 M , VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 6, 2004 |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. all: 74688 / Num. obs: 73866 / % possible obs: 98.9 % / Rmerge(I) obs: 0.101 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.299 / % possible all: 99.9 |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2A9G Resolution: 2.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Displacement parameters | Biso mean: 36 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.38 Å
|