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- PDB-3vbz: Crystal structure of Taipoxin beta subunit isoform 2 -

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Basic information

Entry
Database: PDB / ID: 3vbz
TitleCrystal structure of Taipoxin beta subunit isoform 2
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 / Neutral phospholipase A2 homolog taipoxin beta chain 2
Similarity search - Component
Biological speciesOxyuranus scutellatus scutellatus (Australian taipan)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsCendron, L. / Micetic, I. / Polverino, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipase A2 homolog, taipoxin beta chain
B: Phospholipase A2 homolog, taipoxin beta chain


Theoretical massNumber of molelcules
Total (without water)26,6542
Polymers26,6542
Non-polymers00
Water3,477193
1
A: Phospholipase A2 homolog, taipoxin beta chain


Theoretical massNumber of molelcules
Total (without water)13,3271
Polymers13,3271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phospholipase A2 homolog, taipoxin beta chain


Theoretical massNumber of molelcules
Total (without water)13,3271
Polymers13,3271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-12 kcal/mol
Surface area12050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.570, 36.480, 65.560
Angle α, β, γ (deg.)90.00, 110.09, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 5 / Auth seq-ID: 1 - 118 / Label seq-ID: 1 - 118

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Phospholipase A2 homolog, taipoxin beta chain


Mass: 13327.035 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Oxyuranus scutellatus scutellatus (Australian taipan)
Secretion: venom
References: UniProt: P00615, UniProt: P0CG57*PLUS, phospholipase A2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.21 Å3/Da / Density % sol: 44.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M NaCl, 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: 1.76→33.33 Å / Num. all: 23192 / Num. obs: 23192 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 15.76 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 8.1
Reflection shellResolution: 1.76→1.86 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 2.7 / Num. unique all: 3236 / Rsym value: 0.278 / % possible all: 95.9

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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: PDB ENTRY 1AE7

1ae7


Resolution: 1.76→33.33 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / SU B: 5.668 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.126 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22674 1189 5.1 %RANDOM
Rwork0.1821 ---
all0.18443 23192 --
obs0.18443 22002 98.87 %-
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: 22.737 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å2-0.18 Å2
2---0.05 Å2-0 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.76→33.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1844 0 0 193 2037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0221906
X-RAY DIFFRACTIONr_angle_refined_deg2.0021.9312596
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6585240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.83124.08298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45215300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7711514
X-RAY DIFFRACTIONr_chiral_restr0.1740.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211488
X-RAY DIFFRACTIONr_mcbond_it1.2511.51179
X-RAY DIFFRACTIONr_mcangle_it1.97421896
X-RAY DIFFRACTIONr_scbond_it3.5283727
X-RAY DIFFRACTIONr_scangle_it5.3134.5697
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
468medium positional0.270.5
437loose positional0.625
468medium thermal1.352
437loose thermal1.6810
LS refinement shellResolution: 1.76→1.807 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 79 -
Rwork0.197 1516 -
obs-1516 94.32 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.7247-0.1702-0.90383.31531.06244.19720.0170.3504-0.1117-0.2612-0.0466-0.17590.07790.02850.02950.0741-0.01320.00560.070.01750.07739.6439.7075-32.9588
20.9398-0.04850.20590.45240.06491.39140.00250.16860.0721-0.03580.00580.0451-0.0845-0.0609-0.00830.05-0.0015-0.00170.03860.01910.0584-2.79878.6893-29.0082
32.9367-4.5863-5.85829.57495.66287.8767-0.1894-0.1246-0.01480.52620.1927-0.57020.74420.9519-0.00320.08880.114-0.01160.1655-0.00790.086217.29752.2716-26.489
41.6136-0.35310.62960.9477-0.3282.35980.06450.2065-0.0507-0.0939-0.00620.06890.0755-0.0026-0.05830.0595-0.00790.01190.04670.01090.0790.03945.8929-31.4245
52.3617-1.0293-0.64163.88681.75395.029-0.0048-0.19320.11880.3332-0.02640.0415-0.0402-0.21190.03110.0722-0.00460.0020.0570.01940.0587-2.6825-2.92440.5872
61.0067-0.18590.09150.44740.04431.0533-0.0179-0.1092-0.10040.0171-0.00170.11310.0725-0.20130.01960.0589-0.0098-0.00130.04450.0130.0788-9.3043-2.1847-10.5934
7-1.17491.8737-0.90599.46774.163711.01210.2239-0.2888-0.01410.09910.1769-0.5559-0.46780.5419-0.40080.0451-0.0084-0.00130.1159-0.04040.1197.30254.210.2844
81.69990.06620.16781.37620.13921.5867-0.0413-0.1864-0.03020.0766-0.00340.22130.0333-0.24370.04470.11840.0026-0.00550.10020.01170.1194-8.94160.2677-7.0408
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 17
2X-RAY DIFFRACTION2A18 - 69
3X-RAY DIFFRACTION3A70 - 77
4X-RAY DIFFRACTION4A78 - 118
5X-RAY DIFFRACTION5B1 - 17
6X-RAY DIFFRACTION6B18 - 69
7X-RAY DIFFRACTION7B70 - 77
8X-RAY DIFFRACTION8B78 - 118

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