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

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Basic information

Entry
Database: PDB / ID: 8hav
TitleAn auto-activation mechanism of plant non-specific phospholipase C
ComponentsNon-specific phospholipase C4
KeywordsHYDROLASE / NPC4 / glycosylinositolphosphorylceramide / phosphatidylcholine / phosphate
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
DI(HYDROXYETHYL)ETHER / 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 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)111,7474
Polymers111,5492
Non-polymers1982
Water10,431579
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-17 kcal/mol
Surface area30510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.055, 121.441, 157.383
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 12 through 415)
d_2ens_1chain "B"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1TYRALAA1 - 399
d_21ens_1TYRALAD1 - 399

NCS oper: (Code: givenMatrix: (0.982404914767, 0.028385419115, 0.184593746978), (0.0338903644883, -0.999067909191, -0.0267349213646), (0.183662806895, 0.0325204675118, -0.982451216375)Vector: -6. ...NCS oper: (Code: given
Matrix: (0.982404914767, 0.028385419115, 0.184593746978), (0.0338903644883, -0.999067909191, -0.0267349213646), (0.183662806895, 0.0325204675118, -0.982451216375)
Vector: -6.71088563392, -60.2163600626, 83.2714786751)

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Components

#1: Protein Non-specific phospholipase C4


Mass: 55774.250 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9SRQ7, phospholipase C
#2: 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
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 579 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.53 Å3/Da / Density % sol: 51.38 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Hepes, PEG 3350, Magnesium Chloride Potassium sodium tartrate tetrahydrate
PH range: 7.0 - 8.0

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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→50 Å / Num. obs: 78362 / % possible obs: 99.9 % / Redundancy: 12.88 % / Biso Wilson estimate: 33.54 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.025 / Rrim(I) all: 0.094 / Χ2: 0.99 / Net I/σ(I): 18.9
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 13.49 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 5.8 / Num. unique obs: 4402 / CC1/2: 0.969 / Rpim(I) all: 0.165 / Rrim(I) all: 0.438 / Χ2: 0.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19rc5_4047refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→44.02 Å / SU ML: 0.2021 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.2443
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2089 2000 2.99 %
Rwork0.1818 64897 -
obs0.1826 66897 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.25 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6394 0 13 579 6986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00826613
X-RAY DIFFRACTIONf_angle_d1.03099004
X-RAY DIFFRACTIONf_chiral_restr0.0793934
X-RAY DIFFRACTIONf_plane_restr0.00931188
X-RAY DIFFRACTIONf_dihedral_angle_d6.5815865
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.480350326052 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.24391390.2124536X-RAY DIFFRACTION100
2.15-2.210.28911420.20114603X-RAY DIFFRACTION99.98
2.21-2.280.251410.20484571X-RAY DIFFRACTION99.96
2.28-2.350.22621410.20434565X-RAY DIFFRACTION100
2.35-2.430.25511410.19794578X-RAY DIFFRACTION100
2.43-2.530.23041430.19064605X-RAY DIFFRACTION100
2.53-2.650.20771400.1934588X-RAY DIFFRACTION100
2.65-2.790.24561430.19694621X-RAY DIFFRACTION99.98
2.79-2.960.23351420.19994632X-RAY DIFFRACTION99.96
2.96-3.190.23531430.20184604X-RAY DIFFRACTION100
3.19-3.510.22361440.18194674X-RAY DIFFRACTION99.98
3.51-4.020.19741430.17134664X-RAY DIFFRACTION100
4.02-5.060.14641460.14914731X-RAY DIFFRACTION100
5.06-44.020.19361520.17494925X-RAY DIFFRACTION99.84

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