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- PDB-5vyp: Crystal structure of the Plant Defensin NsD7 bound to PIP2 -

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Basic information

Entry
Database: PDB / ID: 5vyp
TitleCrystal structure of the Plant Defensin NsD7 bound to PIP2
ComponentsDefensin NsD7
KeywordsANTIMICROBIAL PROTEIN / antimicrobial / antifungal / defensin
Function / homology
Function and homology information


phosphatidic acid binding / vacuole / defense response / killing of cells of another organism
Similarity search - Function
Defensin, plant / Gamma-thionins family signature. / Gamma-thionin family / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PIO / Defensin NsD7
Similarity search - Component
Biological speciesNicotiana suaveolens (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsJarva, M. / Lay, F.T. / Hulett, M. / Kvansakul, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)FT130101349 Australia
CitationJournal: FEBS Lett. / Year: 2017
Title: Structure of the defensin NsD7 in complex with PIP2 reveals that defensin : lipid oligomer topologies are dependent on lipid type.
Authors: Jarva, M. / Lay, F.T. / Hulett, M.D. / Kvansakul, M.
History
DepositionMay 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Defensin NsD7
B: Defensin NsD7
C: Defensin NsD7
D: Defensin NsD7
E: Defensin NsD7
F: Defensin NsD7
G: Defensin NsD7
H: Defensin NsD7
I: Defensin NsD7
J: Defensin NsD7
K: Defensin NsD7
L: Defensin NsD7
M: Defensin NsD7
N: Defensin NsD7
O: Defensin NsD7
P: Defensin NsD7
Q: Defensin NsD7
R: Defensin NsD7
S: Defensin NsD7
T: Defensin NsD7
U: Defensin NsD7
V: Defensin NsD7
W: Defensin NsD7
X: Defensin NsD7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,08668
Polymers131,29524
Non-polymers19,79144
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70040 Å2
ΔGint-270 kcal/mol
Surface area44840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.605, 83.489, 105.194
Angle α, β, γ (deg.)90.000, 93.990, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide ...
Defensin NsD7


Mass: 5470.621 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana suaveolens (plant) / Plasmid: pPIC9 / Production host: Komagataella pastoris (fungus) / References: UniProt: C0HK49
#2: Chemical...
ChemComp-PIO / [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate / dioctanoyl l-alpha-phosphatidyl-d-myo-inositol 4,5-diphosphate


Mass: 746.566 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C25H49O19P3
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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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: 2.52 Å3/Da / Density % sol: 51.24 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 9.4 / Details: 20.4% PEG 3350, 0.2M Na-formate, 0.1M CAPS, pH 9.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.6→48.36 Å / Num. obs: 38659 / % possible obs: 96.3 % / Redundancy: 2.7 % / Biso Wilson estimate: 51.69 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.071 / Rrim(I) all: 0.121 / Net I/σ(I): 6.8
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.975 / Num. unique obs: 4760 / CC1/2: 0.51 / Rpim(I) all: 0.725 / Rrim(I) all: 1.222 / % possible all: 97.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.32data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KK4

5kk4


Resolution: 2.6→38.788 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.21
RfactorNum. reflection% reflection
Rfree0.27 1866 4.83 %
Rwork0.2145 --
obs0.2172 38604 95.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 127.42 Å2 / Biso mean: 55.0017 Å2 / Biso min: 23.91 Å2
Refinement stepCycle: final / Resolution: 2.6→38.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8957 0 1240 144 10341
Biso mean--58.47 45.17 -
Num. residues----1145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310417
X-RAY DIFFRACTIONf_angle_d0.63813989
X-RAY DIFFRACTIONf_chiral_restr0.0391505
X-RAY DIFFRACTIONf_plane_restr0.0061599
X-RAY DIFFRACTIONf_dihedral_angle_d16.1436661
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.67030.431380.36642861299997
2.6703-2.74880.40151680.34422814298297
2.7488-2.83750.3941390.31032851299097
2.8375-2.93890.34821410.28732840298197
2.9389-3.05660.35081290.28012883301297
3.0566-3.19560.36541480.27162834298297
3.1956-3.3640.28061570.23962810296796
3.364-3.57460.25241370.20342850298796
3.5746-3.85040.28351320.19242820295295
3.8504-4.23740.22491490.17632798294795
4.2374-4.84960.22051380.15552819295795
4.8496-6.10610.26061310.2012804293594
6.1061-38.79250.20411590.18242754291391

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