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- PDB-3v9m: Phospholipase ACII4 from Australian King Brown Snake -

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Basic information

Entry
Database: PDB / ID: 3v9m
TitlePhospholipase ACII4 from Australian King Brown Snake
ComponentsPhospholipase A2 isozyme PA-11
KeywordsHYDROLASE / wing motif / phospholipase
Function / homology
Function and homology information


phospholipase A2 activity => GO:0004623 / phospholipase A2 activity => GO:0004623 / phospholipase A2 activity / phospholipase A2 / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / 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
DI(HYDROXYETHYL)ETHER / Basic phospholipase A2 PA-11
Similarity search - Component
Biological speciesPseudechis australis (mulga snake)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.563 Å
AuthorsGuddat, L.W. / Millers, E.K.
CitationJournal: To be Published
Title: Mechanistic studies on the anticoagulant activity of a phospholipase A2 from the venom of the Australian King Brown Snake (Pseudechis australis)
Authors: Trabi, M. / Millers, E.-K. / Richards, R. / Snelling, H. / Keegan, R. / Lavin, M.F. / de Jersey, J. / Guddat, L.W. / Masci, P.
History
DepositionDec 27, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phospholipase A2 isozyme PA-11
B: Phospholipase A2 isozyme PA-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,81312
Polymers25,9682
Non-polymers84510
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-78 kcal/mol
Surface area12500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.380, 82.380, 28.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Phospholipase A2 isozyme PA-11 / Phosphatidylcholine 2-acylhydrolase


Mass: 12983.893 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pseudechis australis (mulga snake) / References: UniProt: P04056, phospholipase A2

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Non-polymers , 5 types, 338 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 43.59 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M LITHIUM SULFATE MONOHYDRATE, 0.1M TRIS-HCL, 30% (W/V) PEG 4000, , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 5, 2005
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.56→71.44 Å / Num. all: 28491 / Num. obs: 28491 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.56→1.609 Å / % possible all: 93.99

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.3_473)refinement
CrystalCleardata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.563→22.455 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 24.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2254 1142 4.99 %Random
Rwork0.1877 ---
all0.195 22881 --
obs0.1897 22881 73.67 %-
Solvent computationShrinkage radii: 0.29 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.722 Å2 / ksol: 0.426 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.563→22.455 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1798 0 47 328 2173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091905
X-RAY DIFFRACTIONf_angle_d1.0282559
X-RAY DIFFRACTIONf_dihedral_angle_d13.332693
X-RAY DIFFRACTIONf_chiral_restr0.075248
X-RAY DIFFRACTIONf_plane_restr0.007324
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5631-1.63430.3481150.3018226161
1.6343-1.72040.28441400.2389264672
1.7204-1.82810.31271390.2095270873
1.8281-1.96920.2421440.1929274675
1.9692-2.16720.23711520.1774279776
2.1672-2.48050.20591580.1723282677
2.4805-3.12380.22051450.1784284577
3.1238-22.45760.1861490.1751291079
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2144-0.0948-0.08990.53830.11090.4296-0.0123-0.01170.04430.0660.075-0.04550.0505-0.0617-0.05310.05740.0092-0.01160.0578-0.00130.05331.098231.69354.8215
20.0625-0.1212-0.08710.40170.07070.27940.02060.1419-0.0094-0.0217-0.01320.0921-0.014-0.05560.0090.05360.001-0.0130.0774-0.00980.07350.118919.9366-3.3786
30.06070.0047-0.05170.18840.05470.0786-0.0616-0.0238-0.111-0.0835-0.0550.053-0.0746-0.0120.01690.10080.0243-0.00030.0713-0.00870.0769-1.72238.89068.5545
40.76430.49080.02510.51130.11870.158-0.05040.0110.04260.04110.0534-0.04270.0266-0.0348-0.00890.05380.006-0.00920.058-0.00290.059627.271915.7765-1.5164
50.1558-0.03620.05260.5953-0.26010.2217-0.0314-0.04740.00980.1904-0.0457-0.0238-0.0881-0.06310.05720.09960.0231-0.00350.0875-0.00810.052317.4139.87017.583
60.2468-0.06870.04320.36760.06480.1108-0.04520.1177-0.0002-0.0774-0.0506-0.04070.0138-0.04960.08340.1185-0.00680.01510.1304-0.01930.097533.869317.731-5.5793
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:49)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 50:96)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 97:118)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 1:52)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 53:93)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 94:118)

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