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- PDB-3cyl: Crystal structure of Piratoxin I (a myotoxic Lys49-PLA2) complexe... -

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Basic information

Entry
Database: PDB / ID: 3cyl
TitleCrystal structure of Piratoxin I (a myotoxic Lys49-PLA2) complexed with alpha-tocopherol
ComponentsPhospholipase A2 homolog 2
KeywordsTOXIN / Lys49-PLA2 / Bothrops pirajai / sanke venom / alpha-tocopherol / PrTX-I / Myotoxin / Secreted
Function / homology
Function and homology information


calcium-dependent phospholipase A2 activity / arachidonate secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / phospholipid binding / toxin activity / calcium ion binding / extracellular region
Similarity search - Function
Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain ...Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
VITAMIN E / Basic phospholipase A2 homolog piratoxin-2
Similarity search - Component
Biological speciesBothrops pirajai (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
Authorsdos Santos, J.I. / Fontes, M.R.M.
CitationJournal: J.Struct.Biol. / Year: 2009
Title: Comparative structural studies on Lys49-phospholipases A(2) from Bothrops genus reveal their myotoxic site.
Authors: dos Santos, J.I. / Soares, A.M. / Fontes, M.R.
History
DepositionApr 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipase A2 homolog 2
B: Phospholipase A2 homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,23610
Polymers27,5402
Non-polymers1,6968
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-78 kcal/mol
Surface area11890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.922, 71.369, 44.259
Angle α, β, γ (deg.)90.00, 102.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phospholipase A2 homolog 2 / Piratoxin-II / PrTX-II


Mass: 13770.123 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bothrops pirajai (snake) / References: UniProt: P82287
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-VIT / VITAMIN E / 2,5,7,8-TETRAMETHYL-2-(4,8,12-TRIMETHYLTRIDECYL)-6-CHROMANOL


Mass: 430.706 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H50O2
#4: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% PEG 4000, 0.12M Lithium sulphate, 0.1M TRIS HCl pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.438 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.438 Å / Relative weight: 1
ReflectionResolution: 1.87→26.02 Å / Num. all: 20334 / Num. obs: 19392 / Observed criterion σ(F): 3 / Observed criterion σ(I): 2 / Biso Wilson estimate: 18.6 Å2
Reflection shellResolution: 1.87→1.94 Å

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→26.02 Å / σ(F): 3
RfactorNum. reflection
Rfree0.243 942
Rwork0.183 -
all-20334
obs-19392
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.87→26.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1889 0 111 335 2335
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg2

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