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Yorodumi- PDB-6qsp: Ketosynthase (ApeO) in Complex with its Chain Length Factor (ApeC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qsp | ||||||
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Title | Ketosynthase (ApeO) in Complex with its Chain Length Factor (ApeC) from Xenorhabdus doucetiae | ||||||
Components |
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Keywords | BIOSYNTHETIC PROTEIN / Aryl Polyene Pigment / Biosynthesis / Type II Polyketide Synthase / Ketoacyl Synthase / Chain Elongation / Claisen Condensation | ||||||
Function / homology | Function and homology information beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process Similarity search - Function | ||||||
Biological species | Xenorhabdus doucetiae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Grammbitter, G.L.C. / Schmalhofer, M. / Groll, M. / Bode, H. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2019 Title: An Uncommon Type II PKS Catalyzes Biosynthesis of Aryl Polyene Pigments. Authors: Grammbitter, G.L.C. / Schmalhofer, M. / Karimi, K. / Shi, Y.M. / Schoner, T.A. / Tobias, N.J. / Morgner, N. / Groll, M. / Bode, H.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qsp.cif.gz | 267.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qsp.ent.gz | 214 KB | Display | PDB format |
PDBx/mmJSON format | 6qsp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qs/6qsp ftp://data.pdbj.org/pub/pdb/validation_reports/qs/6qsp | HTTPS FTP |
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-Related structure data
Related structure data | 6qsrC 2iwzS S: Starting model for refinement C: citing same article (ref.) |
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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: 43618.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-Terminal Strep-TEV-Tag / Source: (gene. exp.) Xenorhabdus doucetiae (bacteria) / Gene: XDD1_3472 / Plasmid: pACYC-DUET / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): GOLD(DE3) References: UniProt: A0A068QVX9, beta-ketoacyl-[acyl-carrier-protein] synthase I | ||||
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#2: Protein | Mass: 26474.068 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenorhabdus doucetiae (bacteria) / Gene: XDD1_3460 / Plasmid: pACYC-DUET / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): GOLD(DE3) / References: UniProt: A0A068QZ94 | ||||
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-PO4 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1 M Sodium/Potassium Phosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 26, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→30 Å / Num. obs: 103673 / % possible obs: 98.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.45→1.55 Å / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 2 / % possible all: 96.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2IWZ Resolution: 1.45→30 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.975 / SU B: 2.546 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.055 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.292 Å2
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Refinement step | Cycle: 1 / Resolution: 1.45→30 Å
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Refine LS restraints |
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