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- EMDB-51693: Hemolytic Phospholipase C (PLC H) -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-51693
TitleHemolytic Phospholipase C (PLC H)
Map data
Sample
  • Complex: Hemolytic Phospholipase C (PLC H) and PLC R2
    • Protein or peptide: phospholipase C
  • Ligand: CALCIUM ION
KeywordsHydrolase / Phospholipase C / hemolytic
Function / homology:
Function and homology information
Biological speciesPseudomonas aeruginosa PA14 (bacteria)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 3.5 Å
AuthorsSabharwal NS / Labahn JL
Funding support Germany, 1 items
OrganizationGrant numberCountry
Helmholtz Association Germany
CitationJournal: To Be Published
Title: Structure of Hemolytic Phospholipase C (PLC H)
Authors: Sabharwal NS / Labahn JL
History
DepositionOct 1, 2024-
Header (metadata) releaseOct 15, 2025-
Map releaseOct 15, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51693.png

Downloads & links

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Map

FileDownload / File: emd_51693.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.1162661 - 0.35717136
Average (Standard dev.)-0.0020451378 (±0.01274383)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 217.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51693_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51693_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51693_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Hemolytic Phospholipase C (PLC H) and PLC R2

EntireName: Hemolytic Phospholipase C (PLC H) and PLC R2
Components
  • Complex: Hemolytic Phospholipase C (PLC H) and PLC R2
    • Protein or peptide: phospholipase C
  • Ligand: CALCIUM ION

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Supramolecule #1: Hemolytic Phospholipase C (PLC H) and PLC R2

SupramoleculeName: Hemolytic Phospholipase C (PLC H) and PLC R2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: PLCR2 not observed
Source (natural)Organism: Pseudomonas aeruginosa PA14 (bacteria)
Molecular weightTheoretical: 4.3 kDa/nm

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Macromolecule #1: phospholipase C

MacromoleculeName: phospholipase C / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: phospholipase C
Source (natural)Organism: Pseudomonas aeruginosa PA14 (bacteria)
Molecular weightTheoretical: 84.45868 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SQDPMTENWK FRRRTFLKHG AQAATLAGLS GLFPETLRRA LAIEPDIRTG TIQDVQHVVI LMQENRSFDH YFGHLNGVR GFNDPRALKR QDGKPVWYQN YKYEFSPYHW DTKVTSAQWV SSQNHEWSAF HAIWNQGRND KWMAVQYPEA M GYFKRGDI ...String:
MGSSHHHHHH SQDPMTENWK FRRRTFLKHG AQAATLAGLS GLFPETLRRA LAIEPDIRTG TIQDVQHVVI LMQENRSFDH YFGHLNGVR GFNDPRALKR QDGKPVWYQN YKYEFSPYHW DTKVTSAQWV SSQNHEWSAF HAIWNQGRND KWMAVQYPEA M GYFKRGDI PYYYALADAF TLCEAYHQSM MGP(TPO)NPNRLY HMSGRAAPSG DGKDVHIGND MGDGTIGASG TVDWTTYP E RLSAAGVDWR VYQEGGYRSS SLWYLYVDAY WKYRLQEQNN YDCNALAWFR NFKNAPRDSD LWQRAMLARG VDQLRKDVQ ENTLPQVSWI VAPYCYCEHP WWGPSFGEYY VTRVLDALTS NPEVWARTVF ILNYDEGDGF YDHASAPVPP WKDGVGLSTV STAGEIEAS SGLPIGLGHR VPLIAISPWS KGGKVSAEVF DHTSVLRFLE RRFGVVEENI SPWRRAVCGD LTSLFDFQDA G DTQVAPDL TNVPQSDARK EDAYWQQFYR PSPKYWSYEP KSLPGQEKGQ RPTLAVPYQL HATLALDIAA GKLRLTLGND GM SLPGNPQ GHSAAVFQVQ PREVGNPRFY TVTSYPVVQE SGEELGRTLN DELDDLLDAN GRYAFEVHGP NGFFREFHGN LHL AAQMAR PEVSVTYQRN GNLQLNIRNL GRLPCSVTVT PNPAYTQEGS RRYELEPNQA ISEVWLLRSS QGWYDLSVTA SNTE ANYLR RLAGHVETGK PSRSDPLLDI AAT

UniProtKB: UNIPROTKB: A0A9Q9N6F7

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
StainingType: NEGATIVE / Material: Uranyl acetate
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 15.421 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.25 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 135990
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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