[English] 日本語
![](img/lk-miru.gif)
- PDB-2huf: Crystal structure of Aedes aegypti alanine glyoxylate aminotransferase -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2huf | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Aedes aegypti alanine glyoxylate aminotransferase | ||||||
![]() | Alanine glyoxylate aminotransferase | ||||||
![]() | TRANSFERASE / Alpha and beta protein / PLP-dependent transferase | ||||||
Function / homology | ![]() alanine-glyoxylate transaminase / glycine biosynthetic process, by transamination of glyoxylate / serine-pyruvate transaminase activity / alanine-glyoxylate transaminase activity / glyoxylate catabolic process / peroxisome / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Han, Q. / Robinson, H. / Gao, Y.G. / Vogelaar, N. / Wilson, S.R. / Rizzi, M. / Li, J. | ||||||
![]() | ![]() Title: Crystal Structures of Aedes aegypti Alanine Glyoxylate Aminotransferase. Authors: Han, Q. / Robinson, H. / Gao, Y.G. / Vogelaar, N. / Wilson, S.R. / Rizzi, M. / Li, J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 168.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 131.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 481 KB | Display | |
Data in XML | ![]() | 36 KB | Display | |
Data in CIF | ![]() | 51.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2huiC ![]() 2huuC ![]() 1h0cS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 43390.840 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q3LSM4, alanine-glyoxylate transaminase #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.89 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 12% PEG 8000, 0.13 M magnesium acetate, 4% butanol, 0.1 M cacodylic acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 200 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 21, 2006 |
Radiation | Monochromator: Si(111) or (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→30 Å / Num. obs: 84787 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11 % / Rmerge(I) obs: 0.081 |
Reflection shell | Resolution: 1.75→1.81 Å / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1h0c Resolution: 1.75→29.2 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.903 / SU ML: 0.063 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.577 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→29.2 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.751→1.796 Å / Total num. of bins used: 20
|