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Yorodumi- PDB-8cg6: The ACP crosslinked to the SAT of the cercosporin fungal non-redu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cg6 | |||||||||
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Title | The ACP crosslinked to the SAT of the cercosporin fungal non-reducing polyketide synthase (NR-PKS) CTB1 (ACP:SAT-KS-MAT) | |||||||||
Components |
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Keywords | BIOSYNTHETIC PROTEIN / Fungal non-reducing polyketide synthase (NR-PKS) | |||||||||
Function / homology | Function and homology information : / secondary metabolite biosynthetic process / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / fatty acid biosynthetic process Similarity search - Function | |||||||||
Biological species | Cercospora nicotianae (fungus) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Munoz-Hernandez, H. / Tittes, Y.U. / Maier, T. | |||||||||
Funding support | European Union, Switzerland, 2items
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Citation | Journal: To Be Published Title: CryoEM structure of ACP crosslinked to SAT of the cercosporin fungal non-reducing polyketide synthase (NR-PKS) CTB1 (ACP:SAT-KS-MAT) at 3.4 Angstroms resolution Authors: Munoz-Hernandez, H. / Maier, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cg6.cif.gz | 884.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cg6.ent.gz | 741.3 KB | Display | PDB format |
PDBx/mmJSON format | 8cg6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cg6_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8cg6_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8cg6_validation.xml.gz | 73.4 KB | Display | |
Data in CIF | 8cg6_validation.cif.gz | 111.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cg/8cg6 ftp://data.pdbj.org/pub/pdb/validation_reports/cg/8cg6 | HTTPS FTP |
-Related structure data
Related structure data | 16632MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 140220.000 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cercospora nicotianae (fungus) / Gene: CTB1 / Production host: Escherichia coli (E. coli) References: UniProt: Q6DQW3, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups #2: Protein | | Mass: 9892.837 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Acyl carrier protein (ACP) of Non-reducing polyketide synthase CTB1 Source: (gene. exp.) Cercospora nicotianae (fungus) / Gene: CTB1 / Production host: Escherichia coli (E. coli) References: UniProt: Q6DQW3, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups #3: Chemical | ChemComp-42X / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: ACP crosslinked to the SAT of the starting region of the Non-reducing polyketide synthase CTB1 -SKM- Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Source (natural) | Organism: Cercospora nicotianae (fungus) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 600 nm / Calibrated defocus min: 900 nm / Calibrated defocus max: 3300 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 98 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 6061 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 50 |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 402818 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 105605 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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