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- PDB-8cqm: Broad-range phospholipase C from Listeria monocytogenes -

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Basic information

Entry
Database: PDB / ID: 8cqm
TitleBroad-range phospholipase C from Listeria monocytogenes
ComponentsPhospholipase C
KeywordsHYDROLASE / Zinc-binding / monomer / phospholipase / listeria / lipids / membrane / virulence factor
Function / homology
Function and homology information


phospholipase C / phosphatidylcholine phospholipase C activity / zinc ion binding
Similarity search - Function
Zinc-dependent phospholipase C / Phospholipase C/D / Zinc dependent phospholipase C / Prokaryotic zinc-dependent phospholipase C signature. / Prokaryotic zinc-dependent phospholipase C domain profile. / Zinc dependent phospholipase C (alpha toxin) / Phospholipase C/P1 nuclease domain superfamily
Similarity search - Domain/homology
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsPetrisic, N. / Podobnik, M.
Funding support Slovenia, 2items
OrganizationGrant numberCountry
Slovenian Research AgencyJ1-9174 Slovenia
Slovenian Research AgencyP1-0391 Slovenia
CitationJournal: Nat Commun / Year: 2023
Title: Structural basis for the unique molecular properties of broad-range phospholipase C from Listeria monocytogenes.
Authors: Petrisic, N. / Adamek, M. / Kezar, A. / Hocevar, S.B. / Zagar, E. / Anderluh, G. / Podobnik, M.
History
DepositionMar 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phospholipase C
B: Phospholipase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9069
Polymers55,4332
Non-polymers4737
Water3,477193
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.909, 82.922, 140.815
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 240 or resid 242))
d_2ens_1(chain "B" and (resid 1 through 56 or resid 62 through 76 or resid 81 through 240 or resid 243))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11TRPTRPGLUGLUAA1 - 2381 - 238
d_12GOLGOLGOLGOLAC301
d_21TRPTRPHISHISBB1 - 561 - 56
d_22ASPASPASPASPBB62 - 7662 - 76
d_23PROPROGLUGLUBB81 - 23881 - 238
d_24GOLGOLGOLGOLBG301

NCS oper:
IDCodeMatrixVector
1given(-0.999740602322, -0.0160325812093, 0.0161766624587), (-0.0056483006806, 0.86260406833, 0.505848117521), (-0.0220641058726, 0.50562553104, -0.862470867677)40.6792805484, -1.11388910218, 101.182263453
2given(-0.990440588543, 0.0958133612972, -0.0992332623878), (0.0132984735231, 0.782368256569, 0.622674121603), (0.137297455072, 0.615402072559, -0.776163447942)41.0036256667, -2.93918882011, 91.6263007633

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Components

#1: Protein Phospholipase C / PLC / Lecithinase / Phosphatidylcholine cholinephosphohydrolase


Mass: 27716.740 Da / Num. of mol.: 2 / Mutation: C143S, C168S
Source method: isolated from a genetically manipulated source
Details: gene obtained from genomic isolate of L. monocytogenes
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: plcB, prtC, lmo0205 / Plasmid: pTYB21 / Details (production host): from NEB Impact system / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P33378, phospholipase C
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Fe
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.84 Å3/Da / Density % sol: 33.09 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 8K Na-citrate isopropanol, trimethylamine-N-oxide, phoscholine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1.26 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.26 Å / Relative weight: 1
ReflectionResolution: 2→46.94 Å / Num. obs: 53274 / % possible obs: 99.6 % / Redundancy: 14.5 % / Biso Wilson estimate: 26.91 Å2 / CC1/2: 1 / Rrim(I) all: 0.089 / Net I/σ(I): 27.07
Reflection shellResolution: 2→2.12 Å / Redundancy: 13.5 % / Mean I/σ(I) obs: 4.26 / Num. unique obs: 8615 / CC1/2: 0.934 / Rrim(I) all: 0.0657 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSXDSAPP 2.0data reduction
XDSXDSAPP 2.0data scaling
AutoSol1.19phasing
Coot0.98model building
RefinementMethod to determine structure: SAD / Resolution: 2→41.46 Å / SU ML: 0.2009 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 20.2414
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2089 1090 3.94 %
Rwork0.1744 26591 -
obs0.1758 27681 96.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.44 Å2
Refinement stepCycle: LAST / Resolution: 2→41.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3727 0 17 193 3937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00773841
X-RAY DIFFRACTIONf_angle_d0.90615189
X-RAY DIFFRACTIONf_chiral_restr0.05525
X-RAY DIFFRACTIONf_plane_restr0.0066664
X-RAY DIFFRACTIONf_dihedral_angle_d13.76651388
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.00221779466 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.090.25051290.18613077X-RAY DIFFRACTION91.11
2.09-2.20.20241340.17193229X-RAY DIFFRACTION95.57
2.2-2.340.29331230.2083064X-RAY DIFFRACTION90.57
2.34-2.520.26171360.18793329X-RAY DIFFRACTION97.96
2.52-2.770.2341350.19213358X-RAY DIFFRACTION98.78
2.77-3.170.24531410.18963437X-RAY DIFFRACTION99.64
3.17-40.18111410.16093439X-RAY DIFFRACTION99.39
4-41.460.16611510.1583658X-RAY DIFFRACTION99.92

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