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- PDB-2osh: crystal structure of Natratoxin, a snake sPLA2 that blocks A-type... -

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Basic information

Entry
Database: PDB / ID: 2osh
Titlecrystal structure of Natratoxin, a snake sPLA2 that blocks A-type K+ channel
ComponentsPhospholipase A2 1
KeywordsHYDROLASE / Naja atra venom / PHOSPHOLIPASE A2 / A-type K+ channel inhibitor
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 / toxin activity / calcium ion binding / extracellular region
Similarity search - Function
Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain ...Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Acidic phospholipase A2 natratoxin / Acidic phospholipase A2 1
Similarity search - Component
Biological speciesNaja atra (Chinese cobra)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTeng, M.K. / Sun, L.
CitationJournal: Proteins / Year: 2008
Title: Crystal structure of Natratoxin, a novel snake secreted phospholipaseA2 neurotoxin from Naja atra venom inhibiting A-type K+ currents.
Authors: Hu, P. / Sun, L. / Zhu, Z.Q. / Hou, X.W. / Wang, S. / Yu, S.S. / Wang, H.L. / Zhang, P. / Wang, M. / Niu, L.W. / Teng, M.K. / Ruan, D.Y.
History
DepositionFeb 6, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipase A2 1


Theoretical massNumber of molelcules
Total (without water)13,1161
Polymers13,1161
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.078, 42.078, 64.117
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Phospholipase A2 1 / / Phosphatidylcholine 2-acylhydrolase


Mass: 13115.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Naja atra (Chinese cobra) / Secretion: Venom
References: UniProt: P00598, UniProt: A4FS04*PLUS, phospholipase A2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.16 Å3/Da / Density % sol: 43.14 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.0M Ammonium Sulfate, 5% v/v iso-Propano, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 11, 2006 / Details: mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 5731 / Num. obs: 5557 / % possible obs: 97.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 2.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.2-2.3220.1273.515808090.12798.7
2.32-2.4620.1182.815487850.11898.3
2.46-2.631.90.1640.514017200.16498.6
2.63-2.8420.0763.713676970.07699.4
2.84-3.1120.04214.312066070.04298.7
3.11-3.4820.0494.211625720.04997.6
3.48-4.0220.02919.79864880.02996.6
4.02-4.922.10.02717.68374070.02795.1
4.92-6.962.10.03213.76703130.03292.6
6.96-25.512.20.025243481570.02585

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å25.5 Å
Translation3.5 Å25.5 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
MAR345345DTBdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MF4

1mf4


Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.9 / SU B: 6.232 / SU ML: 0.158 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.357 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.242 266 4.8 %RANDOM
Rwork0.19 ---
obs0.192 5557 96.96 %-
all-5731 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.297 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å20 Å2
2--0.51 Å20 Å2
3----1.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.336 Å0.241 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.202 Å
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms908 0 0 65 973
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022936
X-RAY DIFFRACTIONr_angle_refined_deg1.2441.9281273
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6525118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.07724.78346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.41615138
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.517154
X-RAY DIFFRACTIONr_chiral_restr0.070.2128
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02738
X-RAY DIFFRACTIONr_nbd_refined0.190.2439
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2639
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.255
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3330.212
X-RAY DIFFRACTIONr_mcbond_it0.7061.5607
X-RAY DIFFRACTIONr_mcangle_it1.2052933
X-RAY DIFFRACTIONr_scbond_it1.6863395
X-RAY DIFFRACTIONr_scangle_it2.4364.5340
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 21 -
Rwork0.238 389 -
obs-410 99.03 %

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