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- PDB-9nju: Structure of native homodimer of D. discoideum polyketide synthas... -

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Basic information

Entry
Database: PDB / ID: 9nju
TitleStructure of native homodimer of D. discoideum polyketide synthase Pks16
ComponentsProbable polyketide synthase 16
KeywordsTRANSFERASE / fatty acid synthase activity
Function / homology
Function and homology information


Vitamin B5 (pantothenate) metabolism / Fatty acyl-CoA biosynthesis / sexual reproduction / fatty acid synthase activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / fatty acid biosynthetic process / oxidoreductase activity
Similarity search - Function
Highly reducing polyketide synthase sdgA, C-terminal ACP domain / : / Anamorsin, N-terminal / : / Zinc-binding dehydrogenase / : / Polyketide synthase dehydratase N-terminal domain / : / Polyketide synthase dehydratase domain / Polyketide synthase, dehydratase domain superfamily ...Highly reducing polyketide synthase sdgA, C-terminal ACP domain / : / Anamorsin, N-terminal / : / Zinc-binding dehydrogenase / : / Polyketide synthase dehydratase N-terminal domain / : / Polyketide synthase dehydratase domain / Polyketide synthase, dehydratase domain superfamily / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, enoylreductase domain / Enoylreductase / PKS_KR / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / GroES-like superfamily / Thiolase-like / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Probable polyketide synthase 16
Similarity search - Component
Biological speciesDictyostelium discoideum AX2 (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.94 Å
AuthorsHoogerbrugge, G. / Keatinge-Clay, A.T. / Marcotte, E.M.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM106112 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM122480 United States
Department of Defense (DOD, United States)W911NF-12-1-0390 United States
Welch FoundationF-1712 United States
Welch FoundationF-1515 United States
CitationJournal: To Be Published
Title: Serendipity and the slime mold: a visual survey of megadalton protein assemblies reveals the structure of the polyketide synthase Pks16
Authors: Hoogerbrugge, G. / Keatinge-Clay, A.T. / Marcotte, E.M.
History
DepositionFeb 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable polyketide synthase 16
B: Probable polyketide synthase 16


Theoretical massNumber of molelcules
Total (without water)582,4142
Polymers582,4142
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Probable polyketide synthase 16 / dipks16


Mass: 291206.750 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dictyostelium discoideum AX2 (eukaryote)
References: UniProt: Q869W9, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Has protein modificationN

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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: Homodimer assembly of polyketide synthase Pks16 / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Dictyostelium discoideum AX2 (eukaryote)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 49 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5611 / Symmetry type: POINT
RefinementHighest resolution: 3.94 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00440122
ELECTRON MICROSCOPYf_angle_d0.61554290
ELECTRON MICROSCOPYf_dihedral_angle_d5.8035300
ELECTRON MICROSCOPYf_chiral_restr0.0446164
ELECTRON MICROSCOPYf_plane_restr0.0046992

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