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- PDB-8by8: The cercosporin fungal non-reducing polyketide synthase (NR-PKS) ... -

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Basic information

Entry
Database: PDB / ID: 8by8
TitleThe cercosporin fungal non-reducing polyketide synthase (NR-PKS) CTB1 (SAT-KS-MAT)
ComponentsNon-reducing polyketide synthase CTB1
KeywordsBIOSYNTHETIC PROTEIN / Fungal non-reducing polyketide synthase (NR-PKS)
Function / homology
Function and homology information


phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / fatty acid biosynthetic process
Similarity search - Function
Polyketide product template domain / Polyketide synthase, thioesterase domain / Thioesterase / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Thioesterase / Thioesterase domain / Polyketide synthase, dehydratase domain superfamily / Malonyl-CoA ACP transacylase, ACP-binding ...Polyketide product template domain / Polyketide synthase, thioesterase domain / Thioesterase / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Thioesterase / Thioesterase domain / Polyketide synthase, dehydratase domain superfamily / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Non-reducing polyketide synthase CTB1
Similarity search - Component
Biological speciesCercospora nicotianae (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsMunoz-Hernandez, H. / Maier, T.
Funding supportEuropean Union, Switzerland, 2items
OrganizationGrant numberCountry
European CommissionID: 845941European Union
Swiss National Science Foundation Switzerland
CitationJournal: To Be Published
Title: The cercosporin fungal non-reducing polyketide synthase (NR-PKS) CTB1 (SAT-KS-MAT) at 2.5 Angstroms resolution
Authors: Munoz-Hernandez, H. / Maier, T.
History
DepositionDec 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-reducing polyketide synthase CTB1
B: Non-reducing polyketide synthase CTB1


Theoretical massNumber of molelcules
Total (without water)280,6062
Polymers280,6062
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area12890 Å2
ΔGint-66 kcal/mol
Surface area93900 Å2

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Components

#1: Protein Non-reducing polyketide synthase CTB1 / Cercosporin toxin biosynthesis cluster protein 1


Mass: 140303.062 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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Non-reducing polyketide synthase CTB1 -SKM- / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Cercospora nicotianae (fungus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 165000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 900 nm / Calibrated defocus min: 600 nm / Calibrated defocus max: 3300 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 58 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 8742
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 40

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Processing

SoftwareName: PHENIX / Version: 1.20rc4_4425: / Classification: refinement
EM software
IDNameCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
7PHENIXmodel fitting
8UCSF Chimeramodel fitting
9UCSF ChimeraXmodel fitting
10Cootmodel fitting
12cryoSPARCinitial Euler assignment
13cryoSPARCfinal Euler assignment
14cryoSPARCclassification
15cryoSPARC3D reconstruction
16PHENIXmodel refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1609236 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 6FIJ

6fij


Accession code: 6FIJ / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00239229
ELECTRON MICROSCOPYf_angle_d0.51270879
ELECTRON MICROSCOPYf_dihedral_angle_d16.09610961
ELECTRON MICROSCOPYf_chiral_restr0.0393104
ELECTRON MICROSCOPYf_plane_restr0.0036017

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