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- PDB-8haw: An auto-activation mechanism of plant non-specific phospholipase C -

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Basic information

Entry
Database: PDB / ID: 8haw
TitleAn auto-activation mechanism of plant non-specific phospholipase C
ComponentsNon-specific phospholipase C4
KeywordsHYDROLASE / NPC4 / non-specific phospholipase C / glycosylinositolphosphorylceramide / phosphatidylcholine
Function / homology
Function and homology information


phospholipase C / phosphatidylcholine phospholipase C activity / phospholipase C activity / phospholipid catabolic process / plasma membrane
Similarity search - Function
Phosphoesterase / Phosphoesterase family / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Non-specific phospholipase C4
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsZhao, F. / Fan, R.Y. / Guan, Z.Y. / Guo, L. / Yin, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31570808 China
CitationJournal: Nat Commun / Year: 2023
Title: Insights into the mechanism of phospholipid hydrolysis by plant non-specific phospholipase C.
Authors: Fan, R. / Zhao, F. / Gong, Z. / Chen, Y. / Yang, B. / Zhou, C. / Zhang, J. / Du, Z. / Wang, X. / Yin, P. / Guo, L. / Liu, Z.
History
DepositionOct 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-specific phospholipase C4
B: Non-specific phospholipase C4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,0717
Polymers111,7082
Non-polymers3625
Water14,034779
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.047, 61.621, 132.804
Angle α, β, γ (deg.)90.000, 103.594, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Non-specific phospholipase C4


Mass: 55854.234 Da / Num. of mol.: 2 / Mutation: K178A, K179A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NPC4, At3g03530, T21P5.5 / Plasmid: pET15 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9SRQ7, phospholipase C
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 779 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 46.93 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: PEG 8000, Glycerol, Potassium phosphate monobasic / PH range: 4.5-5.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 58086 / % possible obs: 99.9 % / Redundancy: 6.67 % / Biso Wilson estimate: 19.39 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.047 / Rrim(I) all: 0.12 / Χ2: 0.98 / Net I/σ(I): 10.1
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 6.83 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5.8 / Num. unique obs: 4459 / CC1/2: 0.986 / Rpim(I) all: 0.151 / Rrim(I) all: 0.284 / Χ2: 0.92 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19rc5_4047refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→39.99 Å / SU ML: 0.2004 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.383
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2114 2009 3.47 %
Rwork0.1842 55866 -
obs0.1852 57875 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.66 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7684 0 18 779 8481
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint function
X-RAY DIFFRACTIONf_bond_d0.00247929x
X-RAY DIFFRACTIONf_angle_d0.601810777x
X-RAY DIFFRACTIONf_chiral_restr0.04391122x
X-RAY DIFFRACTIONf_plane_restr0.00441422x
X-RAY DIFFRACTIONf_dihedral_angle_d7.88231046x
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.23661410.18713938X-RAY DIFFRACTION99.88
2.15-2.210.19771440.19353962X-RAY DIFFRACTION99.78
2.21-2.280.24051440.19943951X-RAY DIFFRACTION99.71
2.28-2.350.25241430.19934016X-RAY DIFFRACTION99.71
2.35-2.430.24941430.20443961X-RAY DIFFRACTION99.98
2.43-2.530.24421420.20373998X-RAY DIFFRACTION99.93
2.53-2.650.27231450.1973982X-RAY DIFFRACTION99.93
2.65-2.790.22091450.19513963X-RAY DIFFRACTION99.88
2.79-2.960.23841450.19314018X-RAY DIFFRACTION99.95
2.96-3.190.22351400.19074002X-RAY DIFFRACTION99.98
3.19-3.510.1891420.17594032X-RAY DIFFRACTION99.86
3.51-4.020.17331450.16564007X-RAY DIFFRACTION99.81
4.02-5.060.17441450.15754039X-RAY DIFFRACTION99.79
5.06-100.19331450.18673997X-RAY DIFFRACTION96.35

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