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- PDB-3vc0: Crystal structure of Taipoxin beta subunit isoform 1 -

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Basic information

Entry
Database: PDB / ID: 3vc0
TitleCrystal structure of Taipoxin beta subunit isoform 1
ComponentsPhospholipase A2 homolog, taipoxin beta chain
KeywordsTOXIN / phospholipase A2 fold / PLA2 fold / neurotoxin / phospholipase / Calcium binding / Taipoxin alpha subunit binding / Taipoxin gamma subunit binding / secreted
Function / homology
Function and homology information


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
Neutral phospholipase A2 homolog taipoxin beta chain 1
Similarity search - Component
Biological speciesOxyuranus scutellatus scutellatus (Australian taipan)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsCendron, L. / Micetic, I. / Polverino de Laureto, P. / Beltramini, M. / Paoli, M.
CitationJournal: Febs J. / Year: 2012
Title: Structural analysis of trimeric phospholipase A(2) neurotoxin from the Australian taipan snake venom.
Authors: Cendron, L. / Micetic, I. / Polverino de Laureto, P. / Paoli, M.
History
DepositionJan 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
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 homolog, taipoxin beta chain


Theoretical massNumber of molelcules
Total (without water)13,2511
Polymers13,2511
Non-polymers00
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.890, 76.860, 104.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-233-

HOH

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Components

#1: Protein Phospholipase A2 homolog, taipoxin beta chain


Mass: 13250.916 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oxyuranus scutellatus scutellatus (Australian taipan)
Secretion: venom / References: UniProt: P00615, phospholipase A2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.88 Å3/Da / Density % sol: 57.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.05 M Cadmium sulfate, 0.1 M HEPES Sodium salt, 1.0 M Sodium acetate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.91232 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 18, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91232 Å / Relative weight: 1
ReflectionResolution: 2.15→34.97 Å / Num. all: 8636 / Num. obs: 8636 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 6.3
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 1.6 / Num. unique all: 1239 / Rsym value: 0.443 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AE7

1ae7


Resolution: 2.15→34.97 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.883 / SU B: 11.543 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.203 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2508 406 4.7 %RANDOM
Rwork0.18879 ---
all0.19156 8230 --
obs0.19156 8230 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.737 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å2-0 Å2
2---0.1 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.15→34.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms917 0 0 93 1010
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.021945
X-RAY DIFFRACTIONr_angle_refined_deg1.7911.931281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.615117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.30324.28649
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.13815148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.087156
X-RAY DIFFRACTIONr_chiral_restr0.1180.2128
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021745
X-RAY DIFFRACTIONr_mcbond_it0.9821.5585
X-RAY DIFFRACTIONr_mcangle_it1.7952934
X-RAY DIFFRACTIONr_scbond_it3.2323360
X-RAY DIFFRACTIONr_scangle_it5.134.5347
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 40 -
Rwork0.2 579 -
obs-579 100 %
Refinement TLS params.Method: refined / Origin x: 2.7547 Å / Origin y: -15.454 Å / Origin z: -4.7563 Å
111213212223313233
T0.0065 Å20.0074 Å2-0.003 Å2-0.0346 Å2-0.0122 Å2--0.0451 Å2
L0.7156 °2-0.1108 °2-0.2163 °2-1.6281 °2-0.2047 °2--0.873 °2
S-0.0053 Å °0.0218 Å °-0.0168 Å °-0.0431 Å °0.0072 Å °-0.0427 Å °0.0347 Å °0.0202 Å °-0.0019 Å °

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