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- PDB-8vdb: Crystal structure of Bacillus subtilis FabHB, beta-ketoacyl carri... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8vdb | |||||||||
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Title | Crystal structure of Bacillus subtilis FabHB, beta-ketoacyl carrier protein synthase III | |||||||||
![]() | Beta-ketoacyl-[acyl-carrier-protein] synthase III 2 | |||||||||
![]() | TRANSFERASE / fatty acid biosynthesis / FASII / condensing enzyme | |||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Radka, C.D. / Rock, C.O. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structures of the fatty acid biosynthesis initiation enzymes in Bacillus subtilis. Authors: Radka, C.D. / Rock, C.O. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 261.6 KB | Display | ![]() |
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PDB format | ![]() | 210.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 470.6 KB | Display | ![]() |
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Full document | ![]() | 485.4 KB | Display | |
Data in XML | ![]() | 49.3 KB | Display | |
Data in CIF | ![]() | 69.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8vd9C ![]() 8vdaC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37635.648 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() 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 | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.15 Å3/Da / Density % sol: 70.34 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]()
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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
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Refine LS restraints |
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LS refinement shell |
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