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- PDB-4xs9: Determining the Molecular Basis for Starter Unit Selection During... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4xs9 | ||||||
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Title | Determining the Molecular Basis for Starter Unit Selection During Daunorubicin Biosynthesis | ||||||
![]() | Daunorubicin-doxorubicin polyketide synthase | ||||||
![]() | TRANSFERASE / polyketide / daunorubicin / natural product / starter unit | ||||||
Function / homology | ![]() secondary metabolite biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jackson, D.R. / Valentic, T.R. / Tsai, S.C. / Patel, A. / Mohammed, L. / Vasilakis, K. / Wattana-amorn, P. / Long, P.F. / Crump, M.P. / Crosby, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Determining the Molecular Basis for Starter Unit Selection During Daunorubicin Biosynthesis Authors: Jackson, D.R. / Valentic, T.R. / Tsai, S.C. / Patel, A. / Mohammed, L. / Vasilakis, K. / Wattana-amorn, P. / Long, P.F. / Crump, M.P. / Crosby, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 150.6 KB | Display | ![]() |
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PDB format | ![]() | 116.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4xs7C ![]() 4xsaC ![]() 4xsbC ![]() 4xqp 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 39430.473 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The protein was co-crystallized with a propionyl phosphopantetheine analogue Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q54816, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45 % / Description: hexagonal crystals shaped like Monopoly houses |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.18 M sodium citrate, 26% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 2, 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→38.88 Å / Num. obs: 49899 / % possible obs: 100 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.903 / Mean I/σ(I) obs: 1.75 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4XQP ![]() 4xqp Resolution: 2.002→38.88 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.46 / 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: 2.002→38.88 Å
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Refine LS restraints |
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LS refinement shell |
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