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Yorodumi- PDB-4mz0: Structure of a ketosynthase-acyltransferase di-domain from module... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mz0 | ||||||
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Title | Structure of a ketosynthase-acyltransferase di-domain from module CurL of the curacin A polyketide synthase | ||||||
Components | CurL | ||||||
Keywords | TRANSFERASE / ketosynthase / thiolase fold / acyltransferase / alpha/beta hydrolase fold / Extension of polyketide intermediate | ||||||
Function / homology | Function and homology information S-adenosylmethionine-dependent methyltransferase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Moorea producens 3L (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Whicher, J.R. / Smaga, S.S. / Smith, J.L. | ||||||
Citation | Journal: Chem.Biol. / Year: 2013 Title: Cyanobacterial polyketide synthase docking domains: a tool for engineering natural product biosynthesis. Authors: Whicher, J.R. / Smaga, S.S. / Hansen, D.A. / Brown, W.C. / Gerwick, W.H. / Sherman, D.H. / Smith, J.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mz0.cif.gz | 340.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mz0.ent.gz | 273.5 KB | Display | PDB format |
PDBx/mmJSON format | 4mz0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mz/4mz0 ftp://data.pdbj.org/pub/pdb/validation_reports/mz/4mz0 | HTTPS FTP |
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-Related structure data
Related structure data | 4myyC 4myzC 2qo3S 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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Unit cell |
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-Components
#1: Protein | Mass: 102035.031 Da / Num. of mol.: 2 / Fragment: UNP residues 1-938 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moorea producens 3L (bacteria) / Gene: LYNGBM3L_74440 / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) Strain (production host): BL21 AI containing the pRARE2-CDF plasmid References: UniProt: F4Y424, beta-ketoacyl-[acyl-carrier-protein] synthase I #2: Chemical | #3: 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: 3.02 Å3/Da / Density % sol: 59.24 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 32% PEG 2000, 12% glycerol, 200mM calcium acetate, 100mM Bis-Tris propane pH6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 13, 2011 |
Radiation | Monochromator: double crystal monochromator and K-B pair of biomorph mirrors for vertical and horizontal focusing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 61718 / Num. obs: 61718 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 66.73 Å2 / Rsym value: 0.105 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 6.3 % / Rsym value: 0.69 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2QO3 Resolution: 2.8→40.99 Å / Cor.coef. Fo:Fc: 0.9263 / Cor.coef. Fo:Fc free: 0.8972 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 62.29 Å2
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Refine analyze | Luzzati coordinate error obs: 0.328 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→40.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.87 Å / Total num. of bins used: 20
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