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Yorodumi- PDB-3tzy: Crystal structure of a fragment containing the acyltransferase do... -
+Open data
-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 | ||||||
Components |
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Keywords | TRANSFERASE / Acyltransferase / Long fatty acid chain transferase / Acyl carrier protein | ||||||
Function / homology | Function and homology information polyketide synthase complex / fatty acid elongation, saturated fatty acid / mycolate cell wall layer assembly / mycolic acid biosynthetic process / DIM/DIP cell wall layer assembly / secondary metabolite biosynthetic process / fatty acid synthase activity / acyltransferase activity, transferring groups other than amino-acyl groups / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity ...polyketide synthase complex / fatty acid elongation, saturated fatty acid / mycolate cell wall layer assembly / mycolic acid biosynthetic process / DIM/DIP cell wall layer assembly / secondary metabolite biosynthetic process / fatty acid synthase activity / acyltransferase activity, transferring groups other than amino-acyl groups / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / peptidoglycan-based cell wall / protein homooligomerization / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Bergeret, F. / Pedelacq, J.D. / Mourey, L. / Bon, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tzy.cif.gz | 197.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tzy.ent.gz | 154.3 KB | Display | PDB format |
PDBx/mmJSON format | 3tzy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tzy_validation.pdf.gz | 800.4 KB | Display | wwPDB validaton report |
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Full document | 3tzy_full_validation.pdf.gz | 814.3 KB | Display | |
Data in XML | 3tzy_validation.xml.gz | 37.8 KB | Display | |
Data in CIF | 3tzy_validation.cif.gz | 52.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tz/3tzy ftp://data.pdbj.org/pub/pdb/validation_reports/tz/3tzy | HTTPS FTP |
-Related structure data
Related structure data | 3tzwC 3tzxC 3tzzC 2hg4S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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 |
-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.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv3800c / Plasmid: pWM71, pET28aII / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS References: UniProt: O53579, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups #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) Escherichia coli (E. coli) |
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-Non-polymers , 4 types, 245 molecules
#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Water | ChemComp-HOH / | |
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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: 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: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å |
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: 0.9395 Å / Relative weight: 1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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