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- PDB-9j8s: MprF from Pseudomonas aeruginosa in nanodisc, C2 symmetry -

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Basic information

Entry
Database: PDB / ID: 9j8s
TitleMprF from Pseudomonas aeruginosa in nanodisc, C2 symmetry
ComponentsPhosphatidylglycerol lysyltransferase
KeywordsMEMBRANE PROTEIN / Multiple peptide resistance factor / Membrane Enzyme / Synthase / Flippase / aminoacylated lipid
Function / homology
Function and homology information


lysyltransferase / phosphatidylglycerol alanyltransferase activity / phosphatidylglycerol lysyltransferase activity / phospholipid homeostasis / lipid metabolic process / response to antibiotic / plasma membrane
Similarity search - Function
Lysylphosphatidylglycerol synthetase/glycosyltransferase AglD / Lysylphosphatidylglycerol synthase TM region / : / Phosphatidylglycerol lysyltransferase, C-terminal / Phosphatidylglycerol lysyltransferase, C-terminal / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
Chem-PGT / Phosphatidylglycerol lysyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsJha, S. / Vinothkumar, K.R.
Funding support India, 2items
OrganizationGrant numberCountry
Other governmentDepartment of Atomic Energy, Government of India, RTI 4006
Department of Biotechnology (DBT, India)DBT/PR12422/MED/31/287/2014 India
CitationJournal: To Be Published
Title: Structures of Multiple Peptide Resistance Factor from Pseudomonas aeruginosa
Authors: Jha, S. / Vinothkumar, K.R.
History
DepositionAug 21, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 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: Phosphatidylglycerol lysyltransferase
B: Phosphatidylglycerol lysyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,1678
Polymers196,6612
Non-polymers4,5066
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 Phosphatidylglycerol lysyltransferase / Lysylphosphatidylglycerol synthase / phosphatidylglycerol alanyltransferase


Mass: 98330.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 1-9: MWSHPQFEK - (Strep Tag II), 10-13: GGSG - (Linker), 14-894: PaMprF, 895-899 - Additional residues, 900-903 - VDAL - (N terminus of CPD), 1-32, 716-722, 805-833, 871-881 - Not modelled ...Details: 1-9: MWSHPQFEK - (Strep Tag II), 10-13: GGSG - (Linker), 14-894: PaMprF, 895-899 - Additional residues, 900-903 - VDAL - (N terminus of CPD), 1-32, 716-722, 805-833, 871-881 - Not modelled in MprF (numbering based on Uniprot and doesn't include the fusion construct)
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA0920 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I537, lysyltransferase
#2: Chemical
ChemComp-PGT / (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLGLYCEROL / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)](SODIUM SALT)


Mass: 751.023 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C40H79O10P / Comment: phospholipid*YM
Has ligand of interestN
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: MprF dimer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.18 MDa / Experimental value: NO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria) / Cellular location: Cell membrane
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21 (DE3) C41 / Plasmid: pET22b-CPD
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTrisC4H11NO31
2200 mMSodium ChlorideNaCl1
35 mM2-mercaptoethanolC2H6OS1
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Glow discharge was performed at 25 mA with PELCO easyglow
Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 289 K

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 75000 X / Calibrated magnification: 130481 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 60 sec. / Electron dose: 26.4 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3218
Details: Images were collected in movie-mode at 40 frames per second
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2EPUimage acquisition
4Gctf1.06CTF correction
5RELION4CTF correction
8Coot0.9.8.8model fitting
9UCSF Chimera1.17.3model fitting
11RELION4initial Euler assignment
12cryoSPARC4.3final Euler assignment
13cryoSPARC4.3classification
14cryoSPARC4.33D reconstruction
15PHENIX1.20.1-4487model refinement
16REFMAC5.8.0411model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1701373
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 88069 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 155.5 / Protocol: OTHER
Atomic model buildingAccession code: D_1300050528 / Chain residue range: 33-870
Details: The model from GDN was rigid body fit and manually adjusted for nanodisc map
Source name: Other / Type: experimental model
RefinementResolution: 3.5→139.1 Å / Cor.coef. Fo:Fc: 0.932 / SU B: 20.896 / SU ML: 0.329 / ESU R: 0.698
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rwork0.34748 --
obs0.34748 87748 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 154.156 Å2
Refinement stepCycle: 1 / Total: 12474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0020.01212750
ELECTRON MICROSCOPYr_bond_other_d00.01612876
ELECTRON MICROSCOPYr_angle_refined_deg0.7291.62717312
ELECTRON MICROSCOPYr_angle_other_deg0.2561.55529430
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.57651598
ELECTRON MICROSCOPYr_dihedral_angle_2_deg2.8745124
ELECTRON MICROSCOPYr_dihedral_angle_3_deg14.994102018
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0380.22026
ELECTRON MICROSCOPYr_gen_planes_refined0.0030.0214774
ELECTRON MICROSCOPYr_gen_planes_other0.0010.022986
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it8.23214.6836410
ELECTRON MICROSCOPYr_mcbond_other8.23114.6836410
ELECTRON MICROSCOPYr_mcangle_it13.91626.3928002
ELECTRON MICROSCOPYr_mcangle_other13.91626.3948003
ELECTRON MICROSCOPYr_scbond_it7.89116.2046340
ELECTRON MICROSCOPYr_scbond_other7.89116.2046341
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other14.3729.2569311
ELECTRON MICROSCOPYr_long_range_B_refined21.749136.9614284
ELECTRON MICROSCOPYr_long_range_B_other21.749136.9614285
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.5→3.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork1.3 6495 -
obs--100 %

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