[English] 日本語
![](img/lk-miru.gif)
- PDB-6c85: Crystal structure of aspartate semialdehyde dehydrogenase from Bl... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6c85 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of aspartate semialdehyde dehydrogenase from Blastomyces dermatitidis with p-benzoquinone | ||||||
![]() | Aspartate-semialdehyde dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / Rossman fold / Antifungal inhibitor complex | ||||||
Function / homology | ![]() aspartate-semialdehyde dehydrogenase / aspartate-semialdehyde dehydrogenase activity / threonine biosynthetic process / lysine biosynthetic process via diaminopimelate / NAD binding / NADP binding / protein dimerization activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dahal, G.P. / Viola, R.E. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structural insights into inhibitor binding to a fungal ortholog of aspartate semialdehyde dehydrogenase. Authors: Dahal, G.P. / Viola, R.E. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 144.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 113.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 454.9 KB | Display | |
Data in XML | ![]() | 26.6 KB | Display | |
Data in CIF | ![]() | 36.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6c8wC ![]() 3hskS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 40152.977 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % / Description: long rod-shaped |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2M Ammonium Citrate Tribasic pH 7.0, 18 % w/v PEG 3350 PH range: 6.5-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 24, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→85.8 Å / Num. obs: 59089 / % possible obs: 100 % / Redundancy: 9.7 % / Biso Wilson estimate: 52.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.4→2.47 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 2.96 / Num. unique obs: 4511 / CC1/2: 0.953 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3hsk Resolution: 2.4→71.417 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.58 / Stereochemistry target values: ML
| ||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso max: 150.8 Å2 / Biso mean: 64.6548 Å2 / Biso min: 34.16 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→71.417 Å
|