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- PDB-9f48: KS + AT di-domain of polyketide synthase 13 in Mycobacterium tube... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9f48 | |||||||||
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Title | KS + AT di-domain of polyketide synthase 13 in Mycobacterium tuberculosis | |||||||||
![]() | Polyketide synthase Pks13 | |||||||||
![]() | BIOSYNTHETIC PROTEIN / Mycolic acid synthesis / Claisen condensation / cell wall synthesis | |||||||||
Function / homology | ![]() DIM/DIP cell wall layer assembly / 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 / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Johnston, H.E. / Futterer, K. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: CryoEM structure of the di-domain core of Mycobacterium tuberculosis polyketide synthase 13, essential for mycobacterial mycolic acid synthesis Authors: Johnston, H.E. / Batt, S.M. / Brown, A.K. / Savva, C.G. / Besra, G.S. / Futterer, K. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 458.5 KB | Display | ![]() |
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PDB format | ![]() | 287.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 50185MC M: map data used to model this data 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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1 |
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Components
#1: Protein | Mass: 186642.188 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: pks13, Rv3800c / Production host: ![]() ![]() References: UniProt: I6X8D2, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
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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 |
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Sample preparation
Component | Name: Subunit of Pks13 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.187 MDa / Experimental value: YES |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.9 Details: 20 mM Tris-HCl pH 7.9, 50 mM NaCl, 2.5 mM beta-mercaptoethanol |
Buffer component | Conc.: 20 mM / Name: Tris / Formula: C4H11NO3 |
Specimen | Conc.: 0.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 291 K |
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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: ![]() |
Electron lens | Mode: OTHER / Nominal defocus max: 2700 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 3 sec. / Electron dose: 16.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1412 / Details: movie mode |
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Processing
EM software | Name: PHENIX / Version: 1.21.1_5286 / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 310055 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: OTHER / Num. of particles: 168566 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.54 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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