[English] 日本語
![](img/lk-miru.gif)
- PDB-5kgs: Crystal structure of 7,8-diaminopelargonic acid synthase (BioA) f... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5kgs | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of 7,8-diaminopelargonic acid synthase (BioA) from Mycobacterium tuberculosis, complexed with an inhibitor optimized from HTS lead: 5-[4-(1,3-benzodioxol-5-ylcarbonyl)piperazin-1-yl]-2,3-dihydroinden-1-one | ||||||
![]() | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | ||||||
![]() | Transferase/Transferase inhibitor / transaminase / PLP / Transferase / Transferase-inhibitor complex / Transferase-Transferase inhibitor complex | ||||||
Function / homology | ![]() adenosylmethionine-8-amino-7-oxononanoate transaminase / dethiobiotin synthase activity / adenosylmethionine-8-amino-7-oxononanoate transaminase activity / biotin biosynthetic process / pyridoxal phosphate binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Maize, K.M. / Aldrich, C.C. / Finzel, B.C. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structure-Based Optimization of Pyridoxal 5'-Phosphate-Dependent Transaminase Enzyme (BioA) Inhibitors that Target Biotin Biosynthesis in Mycobacterium tuberculosis. Authors: Liu, F. / Dawadi, S. / Maize, K.M. / Dai, R. / Park, S.W. / Schnappinger, D. / Finzel, B.C. / Aldrich, C.C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 179.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 138.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 4xjoC ![]() 4xjpC ![]() 5kgtC ![]() 4w1xS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 48536.520 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-935 / AF2122/97 / Gene: bioA, Mb1595 / Production host: ![]() ![]() References: UniProt: P0A4X7, adenosylmethionine-8-amino-7-oxononanoate transaminase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.79 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM HEPES, 14% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2015 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.1→203.898 Å / Num. obs: 50729 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 23.82 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.041 / Rrim(I) all: 0.102 / Net I/σ(I): 14.4 / Num. measured all: 317821 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _ / % possible all: 100
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4W1X Resolution: 2.1→46.277 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.74 / 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: 79 Å2 / Biso mean: 22.4997 Å2 / Biso min: 8.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→46.277 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17
|