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Yorodumi- PDB-4jpf: Structure of wild type Pseudomonas aeruginosa FabF (KASII) in Com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jpf | ||||||
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Title | Structure of wild type Pseudomonas aeruginosa FabF (KASII) in Complex with ligand | ||||||
Components | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | ||||||
Keywords | TRANSFERASE / fatty acid biosynthesis / FabF / KASII | ||||||
Function / homology | Function and homology information beta-ketoacyl-[acyl-carrier-protein] synthase II / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.67 Å | ||||||
Authors | Baum, B. / Brenk, R. / Jaenicke, E. | ||||||
Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2015 Title: Structures of Pseudomonas aeruginosa beta-ketoacyl-(acyl-carrier-protein) synthase II (FabF) and a C164Q mutant provide templates for antibacterial drug discovery and identify a buried ...Title: Structures of Pseudomonas aeruginosa beta-ketoacyl-(acyl-carrier-protein) synthase II (FabF) and a C164Q mutant provide templates for antibacterial drug discovery and identify a buried potassium ion and a ligand-binding site that is an artefact of the crystal form. Authors: Baum, B. / Lecker, L.S. / Zoltner, M. / Jaenicke, E. / Schnell, R. / Hunter, W.N. / Brenk, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jpf.cif.gz | 101.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jpf.ent.gz | 74.2 KB | Display | PDB format |
PDBx/mmJSON format | 4jpf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jpf_validation.pdf.gz | 717.4 KB | Display | wwPDB validaton report |
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Full document | 4jpf_full_validation.pdf.gz | 718.5 KB | Display | |
Data in XML | 4jpf_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 4jpf_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jp/4jpf ftp://data.pdbj.org/pub/pdb/validation_reports/jp/4jpf | HTTPS FTP |
-Related structure data
Related structure data | 4b7vSC 4jb6C S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 46102.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: FabF, fabF1, PA2965 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) PlysS References: UniProt: G3XDA2, beta-ketoacyl-[acyl-carrier-protein] synthase II |
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#2: Chemical | ChemComp-1LR / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-K / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2 M Magnesium Chloride, 0.1 M TRIS, 10% (w/v) PEG8000, 5 mM F24, 5% DMSO, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 13, 2013 / Details: Mirrors |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→28.41 Å / Num. obs: 43280 / % possible obs: 99.9 % |
Reflection shell | Resolution: 1.67→1.77 Å / Mean I/σ(I) obs: 2.15 / % possible all: 94.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4b7v, MonomerA Resolution: 1.67→28.41 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.95 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.047 Å2
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Refinement step | Cycle: LAST / Resolution: 1.67→28.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.67→1.71 Å / Total num. of bins used: 20
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