[English] 日本語
![](img/lk-miru.gif)
- PDB-2qo1: 2.6 Angstrom Crystal Structure of the Complex Between 11-(decyldi... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2qo1 | ||||||
---|---|---|---|---|---|---|---|
Title | 2.6 Angstrom Crystal Structure of the Complex Between 11-(decyldithiocarbonyloxy)-undecanoic acid and Mycobacterium Tuberculosis FabH. | ||||||
![]() | 3-oxoacyl-[acyl-carrier-protein] synthase 3 | ||||||
![]() | TRANSFERASE / FATTY ACID BIOSYNTHESIS / MYOBACTERIUM TUBERCULOSIS / STRUCTURAL BASIS FOR SUBSTRATE SPECIFICITY / ENZYME INHIBITOR COMPLEX / MECHANISM BASED INHIBITOR / SUBSTRATE ENTRY AND EXIT / Acyltransferase / Lipid synthesis / Multifunctional enzyme | ||||||
Function / homology | ![]() mycobacterial beta-ketoacyl-[acyl carrier protein] synthase III / beta-ketodecanoyl-[acyl-carrier-protein] synthase activity / long-chain fatty-acyl-CoA metabolic process / beta-ketoacyl-[acyl-carrier-protein] synthase III / beta-ketoacyl-acyl-carrier-protein synthase III activity / fatty-acyl-CoA binding / fatty acid elongation / secondary metabolite biosynthetic process / lipid biosynthetic process / 3-oxoacyl-[acyl-carrier-protein] synthase activity ...mycobacterial beta-ketoacyl-[acyl carrier protein] synthase III / beta-ketodecanoyl-[acyl-carrier-protein] synthase activity / long-chain fatty-acyl-CoA metabolic process / beta-ketoacyl-[acyl-carrier-protein] synthase III / beta-ketoacyl-acyl-carrier-protein synthase III activity / fatty-acyl-CoA binding / fatty acid elongation / secondary metabolite biosynthetic process / lipid biosynthetic process / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sachdeva, S. / Musayev, F. / Alhamadsheh, M. / Scarsdale, J.N. / Wright, H.T. / Reynolds, K.A. | ||||||
![]() | ![]() Title: Separate Entrance and Exit Portals for Ligand Traffic in Mycobacterium tuberculosis FabH Authors: Sachdeva, S. / Musayev, F.N. / Alhamadsheh, M.M. / Scarsdale, J.N. / Wright, H.T. / Reynolds, K.A. #1: ![]() Title: Crystal Structure of the Mycobacterium Tuberculosis Beta-Ketoacyl-Acy; Carrier Protein Synthase III Authors: Muysavev, F. / Sachdeva, S. / Scarsdale, J.N. / Reynolds, K.A. / Wright, H.T. #2: ![]() Title: Crystal Structure of a Substrate Complex of Mycobacterium Tuberculosis Beta-Ketoacyl-Acyl Carrier Protein Sythnase III (FABH) with Lauroyl-Coenzyme A. Authors: Scarsdale, J.N. / Kazanina, G. / He, X. / Reynolds, K.A. / Wright, H.T. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 134.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 103.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 783.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 791.5 KB | Display | |
Data in XML | ![]() | 27.1 KB | Display | |
Data in CIF | ![]() | 36.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2qnxC ![]() 2qnyC ![]() 2qnzC ![]() 2qo0C ![]() 1hzpS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 34903.391 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0A574, UniProt: P9WNG3*PLUS, beta-ketoacyl-[acyl-carrier-protein] synthase I #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.17 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1M NA/K TARTATE, 100MM NA HEPES BUFFER, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 7, 2006 / Details: RIGAKU VARIMAX CONFOCAL OPTICS |
Radiation | Monochromator: RIGAKU VARIMAX OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→39.73 Å / Num. all: 22465 / Num. obs: 20938 / % possible obs: 93.2 % / Redundancy: 2.54 % / Biso Wilson estimate: 43.1 Å2 / Rsym value: 0.108 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 2.84 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 2219 / Rsym value: 0.24 / % possible all: 98.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1HZP Resolution: 2.6→15 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.823 / SU B: 26.637 / SU ML: 0.299 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.425 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: CNS AND REFMAC WERE USED FOR REFINEMENT.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.48 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.388 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→15 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.666 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|