[English] 日本語
![](img/lk-miru.gif)
- PDB-8vd9: Crystal structure of Bacillus subtilis FabHA, beta-ketoacyl carri... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8vd9 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of Bacillus subtilis FabHA, beta-ketoacyl carrier protein synthase III | |||||||||
![]() | Beta-ketoacyl-[acyl-carrier-protein] synthase III 1 | |||||||||
![]() | TRANSFERASE / fatty acid biosynthesis / FASII / condensing enzyme | |||||||||
Function / homology | ![]() branched-chain beta-ketoacyl-[acyl-carrier-protein] synthase / beta-ketodecanoyl-[acyl-carrier-protein] synthase activity / beta-ketoacyl-[acyl-carrier-protein] synthase III / beta-ketoacyl-acyl-carrier-protein synthase III activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Radka, C.D. / Rock, C.O. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Crystal structures of the fatty acid biosynthesis initiation enzymes in Bacillus subtilis. Authors: Radka, C.D. / Rock, C.O. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 76.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 55.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 440.5 KB | Display | |
Data in XML | ![]() | 14.2 KB | Display | |
Data in CIF | ![]() | 19.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8vdaC ![]() 8vdbC C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 34296.141 Da / Num. of mol.: 1 / Mutation: LEU-GLU inserted after MET-1 Source method: isolated from a genetically manipulated source Details: The first three residues (GSH) are from the cleaved affinity tag used to purify the enzyme Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O34746, beta-ketoacyl-[acyl-carrier-protein] synthase III, branched-chain beta-ketoacyl-[acyl-carrier-protein] synthase |
---|---|
#2: Chemical | ChemComp-NHE / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.07 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 50% PEG400, 0.2 mM NaCl, 0.1 M CHES, pH 9.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→61.03 Å / Num. obs: 25612 / % possible obs: 98 % / Redundancy: 16.77 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.077 / Net I/σ(I): 22.99 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 12.34 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 3.87 / Num. unique obs: 1550 / CC1/2: 0.884 / Rrim(I) all: 0.609 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→33.24 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|