[English] 日本語
![](img/lk-miru.gif)
- PDB-6dep: Crystal structure of Candida albicans acetohydroxyacid synthase i... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6dep | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Candida albicans acetohydroxyacid synthase in complex with the herbicide sulfometuron methyl | ||||||
![]() | Acetolactate synthase | ||||||
![]() | transferase/transferase inhibitor / AHAS / acetohydroxyacid synthase / acetolactate synthase / herbicide / thiamin diphosphate / FAD / transferase / sulfometuron methyl / sulfonylurea / transferase-transferase inhibitor complex | ||||||
Function / homology | ![]() acetolactate synthase / acetolactate synthase complex / acetolactate synthase activity / valine biosynthetic process / isoleucine biosynthetic process / thiamine pyrophosphate binding / amino acid biosynthetic process / flavin adenine dinucleotide binding / magnesium ion binding / mitochondrion Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Garcia, M.D. / Guddat, L.W. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Commercial AHAS-inhibiting herbicides are promising drug leads for the treatment of human fungal pathogenic infections. Authors: Garcia, M.D. / Chua, S.M.H. / Low, Y.S. / Lee, Y.T. / Agnew-Francis, K. / Wang, J.G. / Nouwens, A. / Lonhienne, T. / Williams, C.M. / Fraser, J.A. / Guddat, L.W. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 287.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 225 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 30.6 KB | Display | |
Data in CIF | ![]() | 46.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6dekSC ![]() 6delC ![]() 6demC ![]() 6denC ![]() 6deoC ![]() 6deqC ![]() 6derC ![]() 6desC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 74315.367 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: SC5314 / ATCC MYA-2876 / Gene: ILV2, orf19.1613, CAALFM_C302320WA / Plasmid: pET30a(+) / Production host: ![]() ![]() |
---|
-Non-polymers , 7 types, 638 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/K.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/1SM.gif)
![](data/chem/img/TZD.gif)
![](data/chem/img/TP9.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/1SM.gif)
![](data/chem/img/TZD.gif)
![](data/chem/img/TP9.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FAD / |
---|---|
#3: Chemical | ChemComp-K / |
#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-1SM / |
#6: Chemical | ChemComp-TZD / |
#7: Chemical | ChemComp-TP9 / ( |
#8: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 5.37 Å3/Da / Density % sol: 77 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop Details: 1 mM FAD, 1 mM ThDP, 5 mM MgCl2, 5 mM DTT, 3 mM sodium pyruvate, 1 M Na/K tartrate, 0.1 M CHES, and 0.2 M ammonium sulfate, 1 mM sulfometuron methyl PH range: 9.4-9.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 23, 2016 |
Radiation | Monochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.149→48.26 Å / Num. obs: 87576 / % possible obs: 99.7 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.058 / Rrim(I) all: 0.145 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.149→2.19 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4151 / Rpim(I) all: 0.29 / Rrim(I) all: 0.717 / % possible all: 94.2 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6DEK Resolution: 2.149→46.647 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.82
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.149→46.647 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 20.1725 Å / Origin y: 80.4359 Å / Origin z: 75.6768 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |