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- PDB-3tzy: Crystal structure of a fragment containing the acyltransferase do... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3tzy | ||||||
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Title | Crystal structure of a fragment containing the acyltransferase domain of Pks13 from Mycobacterium tuberculosis in the palmitoylated form at 2.2 A | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bergeret, F. / Pedelacq, J.D. / Mourey, L. / Bon, C. | ||||||
![]() | ![]() Title: Biochemical and structural study of the atypical acyltransferase domain from the mycobacterial polyketide synthase pks13 Authors: Bergeret, F. / Gavalda, S. / Chalut, C. / Malaga, W. / Quemard, A. / Pedelacq, J.D. / Daffe, M. / Guilhot, C. / Mourey, L. / Bon, C. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 197.3 KB | Display | ![]() |
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PDB format | ![]() | 154.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3tzwC ![]() 3tzxC ![]() 3tzzC ![]() 2hg4S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Details | THE HETERODIMER FORMED BETWEEN THE UNKNOWN PEPTIDE AND THE ACYLTRANSFERASE DOMAIN OF PKS13 HAS NO KNOWN FUNCTIONAL RELEVANCE FOR THE TIME BEING |
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Components
-Protein / Protein/peptide , 2 types, 4 molecules ABCD
#1: Protein | Mass: 53086.805 Da / Num. of mol.: 2 / Fragment: Acyltransferase domain, UNP residues 576-1062 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: O53579, ![]() #2: Protein/peptide | Mass: 1355.495 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: The author presume that this peptide comes from the Escherichia coli strain that was used to produce the recombinant protein. Source: (natural) ![]() ![]() ![]() |
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-Non-polymers , 4 types, 245 molecules ![](data/chem/img/PLM.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ![]() #4: Chemical | ChemComp-GOL / ![]() #5: Chemical | ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63.19 % |
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Crystal grow![]() | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES, 1.7M ammonium sulfate, 15% glycerol, 1.7% PEG-400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 7, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.2→52.9 Å / Num. obs: 69116 / % possible obs: 91.5 % / Redundancy: 7 % / Biso Wilson estimate: 42.2 Å2 / Rsym value: 0.07 |
Reflection shell | Resolution: 2.2→2.3 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.316 / % possible all: 89.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2HG4 Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.921 / SU B: 6.023 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 44.418 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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