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- PDB-4na2: Crystal Structure of the second ketosynthase from the bacillaene ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4na2 | ||||||
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Title | Crystal Structure of the second ketosynthase from the bacillaene polyketide synthase bound to its natural intermediate | ||||||
![]() | Polyketide synthase PksJ | ||||||
![]() | TRANSFERASE / condensing enzyme fold | ||||||
Function / homology | ![]() : / DIM/DIP cell wall layer assembly / fatty acid synthase activity / secondary metabolite biosynthetic process / ligase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gay, D.C. / Gay, G.R. / Keatinge-Clay, A.T. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 244.5 KB | Display | ![]() |
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PDB format | ![]() | 195.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.4 KB | Display | ![]() |
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Full document | ![]() | 458.3 KB | Display | |
Data in XML | ![]() | 42.9 KB | Display | |
Data in CIF | ![]() | 59.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4na1SC ![]() 4na3C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 70597.188 Da / Num. of mol.: 2 / Fragment: Ketosynthase, UNP residues 3336-3953 / Mutation: C176S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: pksJ, pksK, BSU17180 / Plasmid: pGAY28b / Production host: ![]() ![]() References: UniProt: P40806, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups #2: Water | ChemComp-HOH / | Sequence details | AUTHOR STATES THAT THE GLU TO GLY MUTATION WAS INADVERTEN | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.29 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 15% (w,v) PEG 3350, 0.18 M tri-ammonium citrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 26, 2013 |
Radiation | Monochromator: Double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0331 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→43.5 Å / Num. obs: 60206 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.35→2.393 Å / Rmerge(I) obs: 0.815 / Mean I/σ(I) obs: 2 / % possible all: 87.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4NA1 Resolution: 2.3→43.5 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.909 / Cross valid method: THROUGHOUT / ESU R: 0.394 / ESU R Free: 0.263 / 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: 39.434 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→43.5 Å
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Refine LS restraints |
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