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- PDB-1ae7: NOTEXIN, A PRESYNAPTIC NEUROTOXIC PHOSPHOLIPASE A2 -

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Basic information

Entry
Database: PDB / ID: 1ae7
TitleNOTEXIN, A PRESYNAPTIC NEUROTOXIC PHOSPHOLIPASE A2
ComponentsPHOSPHOLIPASE A2
KeywordsHYDROLASE / PHOSPHOLIPASE A2 / LIPID DEGRADATION / PRESYNAPTIC NEUROTOXIN / VENOM
Function / homology
Function and homology information


calcium-dependent phospholipase A2 activity / phospholipase A2 / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / 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
Basic phospholipase A2 notexin
Similarity search - Component
Biological speciesNotechis scutatus scutatus (cobra)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWesterlund, B. / Nordlund, P. / Uhlin, U. / Eaker, D. / Eklund, H.
CitationJournal: FEBS Lett. / Year: 1992
Title: The three-dimensional structure of notexin, a presynaptic neurotoxic phospholipase A2 at 2.0 A resolution.
Authors: Westerlund, B. / Nordlund, P. / Uhlin, U. / Eaker, D. / Eklund, H.
History
DepositionMar 6, 1997Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9014
Polymers13,6121
Non-polymers2883
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PHOSPHOLIPASE A2
hetero molecules

A: PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8018
Polymers27,2252
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557y,x,-z+21
MethodPQS
Unit cell
Length a, b, c (Å)74.600, 74.600, 49.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PHOSPHOLIPASE A2 / / PLA2 / PHOSPHATIDE SN-2 ACYLHYDROLASE


Mass: 13612.487 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Notechis scutatus scutatus (cobra) / Secretion: VENOM / Species: Notechis scutatus / Strain: scutatus / References: UniProt: P00608, phospholipase A2
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.89 Å3/Da / Density % sol: 57.44 %
Crystal growpH: 7.8
Details: CRYSTALS WERE OBTAINED WHEN A PROTEIN SOLUTION WITH HALF OF THE PRECIPITANT CONCENTRATION OF THE WELL WAS EQUILIBRATED AGAINST 1.4M AMMONIUM SULFATE BUFFERED WITH 50MM CHES-BUFFER AT PH 7.8 ...Details: CRYSTALS WERE OBTAINED WHEN A PROTEIN SOLUTION WITH HALF OF THE PRECIPITANT CONCENTRATION OF THE WELL WAS EQUILIBRATED AGAINST 1.4M AMMONIUM SULFATE BUFFERED WITH 50MM CHES-BUFFER AT PH 7.8 WITH 2% DIOXANE PRESENT
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.4 Mammonium sulphate1reservoir
250 mMCHES-buffer1reservoir
32 %dioxane present1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Sep 1, 1990 / Details: MIRROR
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→5 Å / Num. obs: 10387 / % possible obs: 95 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.063
Reflection shellResolution: 2→2.08 Å / % possible all: 63.4
Reflection
*PLUS
Num. measured all: 32518

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Processing

Software
NameClassification
BUDDAHdata collection
BUDDAHdata reduction
POLARRFNmodel building
X-PLORmodel building
X-PLORrefinement
BUDDHAdata reduction
BUDDHAdata scaling
POLARRFNphasing
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BOVINE PLA2

Resolution: 2→5 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.192 --
obs0.192 9629 94.6 %
Displacement parametersBiso mean: 21.31 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms946 0 15 123 1084
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.608
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.29
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.174
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2→2.08 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.299 804 -
obs--63.4 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARAM19X.PRO
X-RAY DIFFRACTION2PARAM19.SOL
X-RAY DIFFRACTION3TOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.299
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.174

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