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- PDB-2not: NOTECHIS II-5, NEUROTOXIC PHOSPHOLIPASE A2 FROM NOTECHIS SCUTATUS... -

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Basic information

Entry
Database: PDB / ID: 2not
TitleNOTECHIS II-5, NEUROTOXIC PHOSPHOLIPASE A2 FROM NOTECHIS SCUTATUS SCUTATUS
ComponentsPHOSPHOLIPASE A2
KeywordsHYDROLASE / LIPID DEGRADATION / CALCIUM / PRESYNAPTIC NEUROTOXIN / VENOM
Function / homology
Function and homology information


phospholipase A2 / calcium-dependent phospholipase A2 activity / arachidonate secretion / lipid catabolic process / phospholipid metabolic 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 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / 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 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / 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 notechis II-5
Similarity search - Component
Biological speciesNotechis scutatus scutatus (cobra)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsCarredano, E. / Westerlund, B. / Persson, B. / Saarinen, M. / Ramaswamy, S. / Eaker, D. / Eklund, H.
CitationJournal: Toxicon / Year: 1998
Title: The three-dimensional structures of two toxins from snake venom throw light on the anticoagulant and neurotoxic sites of phospholipase A2.
Authors: Carredano, E. / Westerlund, B. / Persson, B. / Saarinen, M. / Ramaswamy, S. / Eaker, D. / Eklund, H.
History
DepositionMar 3, 1997Processing site: BNL
Revision 1.0Jun 16, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_starting_model

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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)27,3932
Polymers27,3932
Non-polymers00
Water18010
1
A: PHOSPHOLIPASE A2


Theoretical massNumber of molelcules
Total (without water)13,6971
Polymers13,6971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PHOSPHOLIPASE A2


Theoretical massNumber of molelcules
Total (without water)13,6971
Polymers13,6971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.500, 43.500, 145.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.3919, 0.92, 0.0051), (0.9127, -0.3881, -0.1282), (-0.116, 0.0549, -0.991)
Vector: -0.1664, 20.1724, 38.7771)

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Components

#1: Protein PHOSPHOLIPASE A2


Mass: 13696.547 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Notechis scutatus scutatus (cobra) / Secretion: VENOM / Species: Notechis scutatus / Strain: scutatus / References: UniProt: P00609, phospholipase A2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.89 %
Description: THE SEQUENCE DIFFERS FROM NOTEXIN'S AT 7 POSITIONS
Crystal growpH: 8.5
Details: THE PROTEIN WAS DISSOLVED IN 50 MM TRIS-NSULFATE, 70MM NH4AC PH 8.5; TO A TOTAL CONCENTRATION OF 15MG/ML; THE PUT IN A THICK-WALLED CAPILLARY SEALED WITH A SEMI-PERMEABLE TUBING AND PLACED ...Details: THE PROTEIN WAS DISSOLVED IN 50 MM TRIS-NSULFATE, 70MM NH4AC PH 8.5; TO A TOTAL CONCENTRATION OF 15MG/ML; THE PUT IN A THICK-WALLED CAPILLARY SEALED WITH A SEMI-PERMEABLE TUBING AND PLACED IN A VESSEL CONTAINING 50MM TRIS-SULFATE, 50NMM NH4AC PH 8.5.N
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMTris-sulfate1drop
270 mM1dropNH4Ac
315 mg/mlprotein1drop
450 mMTris-sulfate1reservoir
550 mM1reservoirNH4Ac

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceType: OTHER / Wavelength: 1.5418
DetectorType: STOE / Detector: DIFFRACTOMETER / Date: Feb 1, 1986
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→15 Å / Num. obs: 4919 / % possible obs: 96.85 % / Observed criterion σ(I): 0 / Redundancy: 1 %
Reflection shellResolution: 3→3.13 Å / Redundancy: 1 % / % possible all: 98.55

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→8 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.255 380 7.5 %RANDOM
Rwork0.219 ---
obs0.219 4539 96.85 %-
Displacement parametersBiso mean: 9.7 Å2
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 0 10 1912
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg2.51
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.75
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
Refine LS restraints NCSNCS model details: UNRESTRICTED
LS refinement shellResolution: 3→3.13 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.284 59 9.5 %
Rwork0.244 550 -
obs--98.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19.PRO
X-RAY DIFFRACTION2PARM19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.2 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.75

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