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Yorodumi- PDB-4ls5: Crystal structure of beta-ketoacyl-ACP synthase II (FabF) from Ba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ls5 | ||||||
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Title | Crystal structure of beta-ketoacyl-ACP synthase II (FabF) from Bacillus subtilis | ||||||
Components | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | ||||||
Keywords | TRANSFERASE / KASII / KETOACYL SYNTHASE / CONDENSING ENZYME / FATTY ACID ELONGATION | ||||||
Function / homology | Function and homology information beta-ketoacyl-[acyl-carrier-protein] synthase II / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | Bacillus subtilis subsp. subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.803 Å | ||||||
Authors | Trajtenberg, F. / Larrieux, N. / Buschiazzo, A. | ||||||
Citation | Journal: Febs J. / Year: 2014 Title: Structural insights into bacterial resistance to cerulenin. Authors: Trajtenberg, F. / Altabe, S. / Larrieux, N. / Ficarra, F. / de Mendoza, D. / Buschiazzo, A. / Schujman, G.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ls5.cif.gz | 337.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ls5.ent.gz | 274 KB | Display | PDB format |
PDBx/mmJSON format | 4ls5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/4ls5 ftp://data.pdbj.org/pub/pdb/validation_reports/ls/4ls5 | HTTPS FTP |
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-Related structure data
Related structure data | 4ls6C 4ls7C 4ls8C 2gqdS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 45609.285 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria) Strain: 168 / Gene: fabF, yjaY, BSU11340 / Plasmid: pQE32L / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 References: UniProt: O34340, beta-ketoacyl-[acyl-carrier-protein] synthase II #2: Chemical | ChemComp-K / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.11 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 10% PEG3350, 0.25 M KCl , pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 5, 2008 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: multilayer mirrors (Varimax-HF) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.803→74.879 Å / Num. all: 85353 / Num. obs: 85353 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 23.31 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 13.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2GQD Resolution: 1.803→28.977 Å / Occupancy max: 1 / Occupancy min: 0.11 / FOM work R set: 0.8726 / SU ML: 0.2 / σ(F): 0.91 / Phase error: 20.19 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.74 Å2 / Biso mean: 28.5391 Å2 / Biso min: 8.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.803→28.977 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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