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Yorodumi- PDB-4na3: Crystal Structure of the second ketosynthase from the bacillaene ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4na3 | ||||||
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Title | Crystal Structure of the second ketosynthase from the bacillaene polyketide synthase bound to a hexanoyl substrate mimic | ||||||
Components | Polyketide synthase PksJ | ||||||
Keywords | TRANSFERASE / condensing enzyme fold | ||||||
Function / homology | Function and homology information DIM/DIP cell wall layer assembly / organonitrogen compound biosynthetic process / fatty acid synthase activity / phosphopantetheine binding / ligase activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis subsp. subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å | ||||||
Authors | Gay, D.C. / Gay, G.R. / Keatinge-Clay, A.T. | ||||||
Citation | Journal: Structure / Year: 2014 Title: A close look at a ketosynthase from a trans-acyltransferase modular polyketide synthase. Authors: Gay, D.C. / Gay, G. / Axelrod, A.J. / Jenner, M. / Kohlhaas, C. / Kampa, A. / Oldham, N.J. / Piel, J. / Keatinge-Clay, A.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4na3.cif.gz | 242.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4na3.ent.gz | 193.4 KB | Display | PDB format |
PDBx/mmJSON format | 4na3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/na/4na3 ftp://data.pdbj.org/pub/pdb/validation_reports/na/4na3 | HTTPS FTP |
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-Related structure data
Related structure data | 4na1SC 4na2C 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
#1: Protein | Mass: 70496.086 Da / Num. of mol.: 2 / Fragment: Ketosynthase, UNP residues 3336-3953 / Mutation: C176S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria) Strain: 168 / Gene: pksJ, pksK, BSU17180 / Plasmid: pGAY28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P40806, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Sequence details | AUTHOR STATES THAT THE GLU TO GLY MUTATION WAS INADVERTEN | |
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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: 2.89 Å3/Da / Density % sol: 57.47 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 1.1 M ammonium sulfate, 0.2 M lithium sulfate, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 3, 2013 |
Radiation | Monochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.83→33.7 Å / Num. all: 35693 / Num. obs: 35693 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.9→2.978 Å / Rmerge(I) obs: 0.017 / % possible all: 82 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4NA1 Resolution: 2.89→33.7 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.914 / Cross valid method: THROUGHOUT / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 59.77 Å2
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Refinement step | Cycle: LAST / Resolution: 2.89→33.7 Å
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Refine LS restraints |
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