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- PDB-9gye: Hemolytic Phospholipase C (PLC H) -

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Basic information

Entry
Database: PDB / ID: 9gye
TitleHemolytic Phospholipase C (PLC H)
Componentsphospholipase C
KeywordsHYDROLASE / Phospholipase C / hemolytic
Function / homology:
Function and homology information
Biological speciesPseudomonas aeruginosa PA14 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / negative staining / cryo EM / Resolution: 3.5 Å
AuthorsSabharwal, N.S. / Labahn, J.L.
Funding support Germany, 1items
OrganizationGrant numberCountry
Helmholtz Association Germany
CitationJournal: To Be Published
Title: Structure of Hemolytic Phospholipase C (PLC H)
Authors: Sabharwal, N.S. / Labahn, J.L.
History
DepositionOct 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 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: phospholipase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4992
Polymers84,4591
Non-polymers401
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 phospholipase C


Mass: 84458.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PA14 (bacteria) / Gene: N8E94_21890 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A9Q9N6F7, phospholipase C
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
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: Hemolytic Phospholipase C (PLC H) and PLC R2 / Type: COMPLEX / Details: PLCR2 not observed / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 4.3 kDa/nm / Experimental value: YES
Source (natural)Organism: Pseudomonas aeruginosa PA14 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: YES
EM stainingType: NEGATIVE / Material: Uranyl acetate
VitrificationCryogen name: ETHANE-PROPANE

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2250 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 15.421 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 135990 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0045672
ELECTRON MICROSCOPYf_angle_d0.7087738
ELECTRON MICROSCOPYf_dihedral_angle_d5.729773
ELECTRON MICROSCOPYf_chiral_restr0.047783
ELECTRON MICROSCOPYf_plane_restr0.0051025

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