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Yorodumi- PDB-8vd9: Crystal structure of Bacillus subtilis FabHA, beta-ketoacyl carri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vd9 | |||||||||
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Title | Crystal structure of Bacillus subtilis FabHA, beta-ketoacyl carrier protein synthase III | |||||||||
Components | Beta-ketoacyl-[acyl-carrier-protein] synthase III 1 | |||||||||
Keywords | TRANSFERASE / fatty acid biosynthesis / FASII / condensing enzyme | |||||||||
Function / homology | Function and homology information 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 | Bacillus subtilis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | |||||||||
Authors | Radka, C.D. / Rock, C.O. | |||||||||
Funding support | United States, 2items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8vd9.cif.gz | 76.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vd9.ent.gz | 55.4 KB | Display | PDB format |
PDBx/mmJSON format | 8vd9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vd/8vd9 ftp://data.pdbj.org/pub/pdb/validation_reports/vd/8vd9 | HTTPS FTP |
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-Related structure data
Related structure data | 8vdaC 8vdbC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-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.) Bacillus subtilis (bacteria) / Gene: fabHA, fabH, fabH1, yjaX, BSU11330 / Production host: Escherichia coli (E. coli) References: UniProt: O34746, beta-ketoacyl-[acyl-carrier-protein] synthase III, branched-chain beta-ketoacyl-[acyl-carrier-protein] synthase |
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#2: Chemical | ChemComp-NHE / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.07 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
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 |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→33.24 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.51 / Phase error: 24.82 / Stereochemistry target values: ML
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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: 1.85→33.24 Å
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Refine LS restraints |
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LS refinement shell |
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