[English] 日本語
Yorodumi- PDB-8vdb: Crystal structure of Bacillus subtilis FabHB, beta-ketoacyl carri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vdb | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of Bacillus subtilis FabHB, beta-ketoacyl carrier protein synthase III | |||||||||
Components | Beta-ketoacyl-[acyl-carrier-protein] synthase III 2 | |||||||||
Keywords | TRANSFERASE / fatty acid biosynthesis / FASII / condensing enzyme | |||||||||
Function / homology | Function and homology information branched-chain beta-ketoacyl-[acyl-carrier-protein] synthase / beta-ketoacyl-[acyl-carrier-protein] synthase III / beta-ketoacyl-acyl-carrier-protein synthase III activity / secondary metabolite biosynthetic process / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytoplasm Similarity search - Function | |||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Radka, C.D. / Rock, C.O. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: J.Struct.Biol. / Year: 2024 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: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8vdb.cif.gz | 261.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8vdb.ent.gz | 210.4 KB | Display | PDB format |
PDBx/mmJSON format | 8vdb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vdb_validation.pdf.gz | 470.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8vdb_full_validation.pdf.gz | 485.4 KB | Display | |
Data in XML | 8vdb_validation.xml.gz | 49.3 KB | Display | |
Data in CIF | 8vdb_validation.cif.gz | 69.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vd/8vdb ftp://data.pdbj.org/pub/pdb/validation_reports/vd/8vdb | HTTPS FTP |
-Related structure data
Related structure data | 8vd9C 8vdaC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 37635.648 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: fabHB, fabH2, yhfB, BSU10170 / Production host: Escherichia coli (E. coli) References: UniProt: O07600, beta-ketoacyl-[acyl-carrier-protein] synthase III, branched-chain beta-ketoacyl-[acyl-carrier-protein] synthase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.15 Å3/Da / Density % sol: 70.34 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 20% MPD, 0.1 M HEPES, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→77.14 Å / Num. obs: 88179 / % possible obs: 93.2 % / Redundancy: 3.8 % / CC1/2: 0.983 / Rmerge(I) obs: 0.156 / Rrim(I) all: 0.182 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.874 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4618 / CC1/2: 0.743 / % possible all: 94.1 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→45.2 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 27.43 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→45.2 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|