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- PDB-1vap: THE MONOMERIC ASP49 SECRETORY PHOSPHOLIPASE A2 FROM THE VENOM OF ... -

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Basic information

Entry
Database: PDB / ID: 1vap
TitleTHE MONOMERIC ASP49 SECRETORY PHOSPHOLIPASE A2 FROM THE VENOM OF AGKISTRIDON PISCIVORUS PISCIVORUS
ComponentsPHOSPHOLIPASE A2
KeywordsLIPID DEGRADATION / PHOSPHOLIPASE A2 / HYDROLASE
Function / homology
Function and homology information


phospholipase A2 activity => GO:0004623 / phospholipase A2 activity => GO:0004623 / phospholipase A2 / phospholipase A2 activity / 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
Basic phospholipase A2 APP-D49
Similarity search - Component
Biological speciesAgkistrodon piscivorus piscivorus (Eastern cottonmouth)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsScott, D.L.
CitationJournal: J.Biol.Chem. / Year: 1997
Title: Structural aspects of interfacial adsorption. A crystallographic and site-directed mutagenesis study of the phospholipase A2 from the venom of Agkistrodon piscivorus piscivorus.
Authors: Han, S.K. / Yoon, E.T. / Scott, D.L. / Sigler, P.B. / Cho, W.
History
DepositionNov 15, 1996-
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 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
B: PHOSPHOLIPASE A2


Theoretical massNumber of molelcules
Total (without water)28,0182
Polymers28,0182
Non-polymers00
Water2,504139
1
A: PHOSPHOLIPASE A2


Theoretical massNumber of molelcules
Total (without water)14,0091
Polymers14,0091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PHOSPHOLIPASE A2


Theoretical massNumber of molelcules
Total (without water)14,0091
Polymers14,0091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.710, 39.890, 42.850
Angle α, β, γ (deg.)94.17, 79.10, 106.27
Int Tables number1
Space group name H-MP1

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Components

#1: Protein PHOSPHOLIPASE A2 /


Mass: 14009.135 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: SECRETORY PHOSPHOLIPASE A2
Source: (natural) Agkistrodon piscivorus piscivorus (Eastern cottonmouth)
Species: Agkistrodon piscivorus / Strain: piscivorus / References: UniProt: P51972, phospholipase A2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.34 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.03 mg/mlApp-D491drop
220 %(v/v)ethanol1drop
30.1 MTris-HCl1drop
440 %(v/v)ethanol1reservoir
50.2 MTris-HCl1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Dec 4, 1990
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 28084 / % possible obs: 82 % / Rmerge(I) obs: 0.042
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 99 Å

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Processing

Software
NameVersionClassification
HAMLINSOFTWARE SUITEdata collection
X-PLORmodel building
PROFFTrefinement
X-PLORrefinement
HAMLINdata reduction
X-PLORphasing
RefinementResolution: 1.6→10 Å / σ(F): 1.5 /
RfactorNum. reflection
Rwork0.197 -
obs-21410
Displacement parametersBiso mean: 22.1 Å2
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1942 0 0 139 2081
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.012
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0270.02
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0250.05
X-RAY DIFFRACTIONp_chiral_restr0.2130.5
X-RAY DIFFRACTIONp_singtor_nbd0.1652
X-RAY DIFFRACTIONp_multtor_nbd0.2652
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.630
X-RAY DIFFRACTIONp_staggered_tor20.6500
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor30.9500
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS

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