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- PDB-8f7h: The condensation domain of surfactin A synthetase C variant 18b i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8f7h | ||||||
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Title | The condensation domain of surfactin A synthetase C variant 18b in space group P212121 | ||||||
![]() | Surfactin synthetase | ||||||
![]() | BIOSYNTHETIC PROTEIN / NRPS / C domain / SrfA-C | ||||||
Function / homology | ![]() amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / phosphopantetheine binding / catalytic activity / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Frota, N.F. / Pistofidis, A. / Folger, I.B. / Hilvert, D. / Schmeing, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: High-throughput reprogramming of an NRPS condensation domain. Authors: Ines B Folger / Natália F Frota / Angelos Pistofidis / David L Niquille / Douglas A Hansen / T Martin Schmeing / Donald Hilvert / ![]() ![]() Abstract: Engineered biosynthetic assembly lines could revolutionize the sustainable production of bioactive natural product analogs. Although yeast display is a proven, powerful tool for altering the ...Engineered biosynthetic assembly lines could revolutionize the sustainable production of bioactive natural product analogs. Although yeast display is a proven, powerful tool for altering the substrate specificity of gatekeeper adenylation domains in nonribosomal peptide synthetases (NRPSs), comparable strategies for other components of these megaenzymes have not been described. Here we report a high-throughput approach for engineering condensation (C) domains responsible for peptide elongation. We show that a 120-kDa NRPS module, displayed in functional form on yeast, can productively interact with an upstream module, provided in solution, to produce amide products tethered to the yeast surface. Using this system to screen a large C-domain library, we reprogrammed a surfactin synthetase module to accept a fatty acid donor, increasing catalytic efficiency for this noncanonical substrate >40-fold. Because C domains can function as selectivity filters in NRPSs, this methodology should facilitate the precision engineering of these molecular assembly lines. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 327.6 KB | Display | ![]() |
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PDB format | ![]() | 223.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 688.6 KB | Display | ![]() |
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Full document | ![]() | 694.3 KB | Display | |
Data in XML | ![]() | 18.8 KB | Display | |
Data in CIF | ![]() | 26.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8f7fC ![]() 8f7gC ![]() 8f7iC ![]() 2vsqS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 53579.785 Da / Num. of mol.: 1 / Fragment: Condensation domain, residues 7-441 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.87 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 0.04 M KH2PO4, 16 %w/v PEG 8K and 20% (v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 19, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 43869 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 44.46 Å2 / CC1/2: 0.998 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 13.5 % / Num. unique obs: 2156 / CC1/2: 0.39 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2VSQ Resolution: 1.93→47.09 Å / SU ML: 0.2303 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.217 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.86 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.93→47.09 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 1.44722901559 Å / Origin y: -4.99347587703 Å / Origin z: -5.01156963979 Å
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Refinement TLS group | Selection details: all |