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- PDB-9pqy: Structure of ACP domain conjugated with stearic acid and interact... -

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Basic information

Entry
Database: PDB / ID: 9pqy
TitleStructure of ACP domain conjugated with stearic acid and interacting with MPT domain from M. tuberculosis type-I FAS
Components
  • 3-oxoacyl-ACP synthase
  • Fatty acid synthase
KeywordsBIOSYNTHETIC PROTEIN / Fatty acid synthase
Function / homology
Function and homology information


fatty acid synthase complex / beta-ketoacyl-[acyl-carrier-protein] synthase I / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid synthase activity / fatty acid biosynthetic process / hydrolase activity
Similarity search - Function
: / Fatty acid synthase central AT domain / DNA polymerase beta N-terminal domain / Fatty acid synthase beta subunit AflB /Fas1-like, central domain / Fatty acid synthase subunit beta/Fas1-like, helical / : / : / Fatty acid synthase / MaoC-like dehydratase domain / MaoC like domain ...: / Fatty acid synthase central AT domain / DNA polymerase beta N-terminal domain / Fatty acid synthase beta subunit AflB /Fas1-like, central domain / Fatty acid synthase subunit beta/Fas1-like, helical / : / : / Fatty acid synthase / MaoC-like dehydratase domain / MaoC like domain / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / HotDog domain superfamily / 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 / Thiolase-like / Aldolase-type TIM barrel / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
3-oxoacyl-ACP synthase / Fatty acid synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.51 Å
AuthorsMazhab-Jafari, M.T. / Samani, E.K.
Funding support Canada, 3items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)195698 Canada
Canadian Institutes of Health Research (CIHR)419240 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-06070 Canada
CitationJournal: To Be Published
Title: Structural basis of product recognition by Mycobacterium Tuberculosis fatty acid synthase
Authors: Samani, E.K. / Mazhab-Jafari, M.T.
History
DepositionJul 23, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 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: 3-oxoacyl-ACP synthase
B: Fatty acid synthase


Theoretical massNumber of molelcules
Total (without water)653,8242
Polymers653,8242
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein 3-oxoacyl-ACP synthase / 3-oxoacyl-[acyl-carrier-protein] synthase 1 / Fatty acid synthase / Type I polyketide synthase


Mass: 326601.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: kasA_2, A4S10_02647, DKC2_2660, DSJ38_17120, ERS094118_02070, SAMEA2682864_02566
Production host: Escherichia coli (E. coli)
References: UniProt: A0A9P1LAJ1, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Protein Fatty acid synthase


Mass: 327222.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: fas, J8J21_09265 / Production host: Escherichia coli (E. coli) / References: UniProt: A0ABD4PYJ0
Has ligand of interestY
Has protein modificationY

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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: Fatty acid synthase / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 1.8 MDa / Experimental value: YES
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM / Grid mesh size: 400 divisions/in. / Grid type: Homemade
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 35 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 458280
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45089 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 6GJC

6gjc


Accession code: 6GJC / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.51 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0034554
ELECTRON MICROSCOPYf_angle_d0.5076177
ELECTRON MICROSCOPYf_dihedral_angle_d5.768660
ELECTRON MICROSCOPYf_chiral_restr0.037707
ELECTRON MICROSCOPYf_plane_restr0.003808

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