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- PDB-4yz7: Crystal structure of Piratoxin I (PrTX-I) complexed to aristoloch... -

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Basic information

Entry
Database: PDB / ID: 4yz7
TitleCrystal structure of Piratoxin I (PrTX-I) complexed to aristolochic acid
ComponentsBasic phospholipase A2 homolog piratoxin-1
KeywordsTOXIN / phospholipase A2 / phospholipase A2-like / inhibitor
Function / homology
Function and homology information


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 / 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
9-HYDROXY ARISTOLOCHIC ACID / Basic phospholipase A2 homolog piratoxin-1
Similarity search - Component
Biological speciesBothrops pirajai (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9589 Å
AuthorsFernandes, C.A.H. / Fontes, M.R.M.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2009/10905-5 Brazil
Sao Paulo Research Foundation (FAPESP)2013/17864-8 Brazil
CitationJournal: Plos One / Year: 2015
Title: Structural Basis for the Inhibition of a Phospholipase A2-Like Toxin by Caffeic and Aristolochic Acids.
Authors: Fernandes, C.A. / Cardoso, F.F. / Cavalcante, W.G. / Soares, A.M. / Dal-Pai, M. / Gallacci, M. / Fontes, M.R.
History
DepositionMar 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Derived calculations
Category: pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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: Basic phospholipase A2 homolog piratoxin-1
B: Basic phospholipase A2 homolog piratoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7009
Polymers27,5082
Non-polymers1,1927
Water3,135174
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.317, 70.931, 44.048
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsDimer confirmed by dynamic light scattering

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Components

#1: Protein Basic phospholipase A2 homolog piratoxin-1 / svPLA2 homolog / Myotoxin SIV-SP5 / Piratoxin-I / PrTX-I


Mass: 13754.101 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bothrops pirajai (snake) / References: UniProt: P58399
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 / Polyethylene glycol


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#4: Chemical ChemComp-9AR / 9-HYDROXY ARISTOLOCHIC ACID / 9-HYDROXY-8-METHOXY-6-NITRO-PHENANTHROL[3,4-D][1,3]DIOXOLE-5-CARBOXYLIC ACID


Mass: 357.271 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H11NO8
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.1 / Details: PEG 4000, Tris HCl pH 8.1 and lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.437 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.437 Å / Relative weight: 1
ReflectionResolution: 1.95→25.61 Å / Num. obs: 15848 / % possible obs: 99.22 % / Redundancy: 3 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 5.29
Reflection shellRmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.23 / Num. unique all: 1541 / % possible all: 98.59

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CYL

3cyl


Resolution: 1.9589→25.61 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0.2 / Phase error: 23.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2352 786 4.96 %
Rwork0.173 --
obs0.1762 15842 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9589→25.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1749 0 60 174 1983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071854
X-RAY DIFFRACTIONf_angle_d1.1382499
X-RAY DIFFRACTIONf_dihedral_angle_d12.242646
X-RAY DIFFRACTIONf_chiral_restr0.072262
X-RAY DIFFRACTIONf_plane_restr0.005320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9589-2.08150.28911270.2122449X-RAY DIFFRACTION99
2.0815-2.24220.25641320.1782461X-RAY DIFFRACTION99
2.2422-2.46760.25031090.17282513X-RAY DIFFRACTION99
2.4676-2.82430.26641440.17812474X-RAY DIFFRACTION99
2.8243-3.55680.2491210.17172532X-RAY DIFFRACTION99
3.5568-25.61210.20251530.16552627X-RAY DIFFRACTION99
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)
11.82881.21420.68253.1716-0.46430.7788-0.1177-0.1812-0.2351-0.7790.2378-0.8107-0.3856-0.0214-0.05360.2913-0.00770.11170.2163-0.0690.210726.55713.393715.0875
23.6352-1.0199-1.99313.4475-1.0371.88750.13510.09880.6026-0.2972-0.20190.54540.1954-0.52940.06960.17440.0215-0.06140.2738-0.05130.259411.22063.879416.6083
31.9765-0.5622-0.02335.74290.03212.512-0.013-0.08280.0469-0.3438-0.06210.2394-0.2985-0.80.06480.21960.0221-0.02990.2395-0.03230.167615.32629.126621.0977
43.10141.61960.32582.90412.35762.34770.02450.14920.9273-1.02230.2262-0.378-1.1841-0.05250.07710.54560.14780.06770.19430.030.352421.907120.526115.3477
54.26433.628-2.12213.88510.15935.89430.04820.42390.3908-0.02220.2233-0.5206-0.6520.42840.26010.3668-0.03450.23710.21420.0580.510232.921414.336217.7117
60.31510.2414-0.12880.7062-0.97781.56590.1169-0.20280.27440.3992-0.18370.0148-0.27210.58290.28780.2324-0.02660.02850.3013-0.11690.580236.55024.571924.8709
70.2343-0.1168-0.19450.21380.36160.6062-0.0456-0.13420.9351-0.1259-0.4277-0.3685-0.4798-0.06220.27210.2449-0.0692-0.02890.2123-0.02730.792132.451317.372522.739
81.54330.41570.27171.96631.16661.1919-0.072-0.130.36730.0519-0.1113-0.2343-0.2125-0.00920.06190.1650.0191-0.02490.1683-0.03330.262325.073111.273623.1391
90.72490.0892-0.05453.46610.79953.43770.075-0.0651-0.1307-0.2566-0.05060.59710.7620.0372-0.13360.3099-0.0064-0.00950.23260.03190.214816.1438-5.752319.5151
100.3091.04620.16353.58690.66453.0761-0.06590.13970.16360.1945-0.11230.4719-0.2127-0.44340.49250.2933-0.0564-0.03430.3178-0.0731-0.00339.7756-0.948610.201
118.29291.9453-0.05535.0691-3.81013.12770.2645-0.49480.34440.6447-0.21280.5657-0.1449-0.97130.86260.14940.0334-0.0770.41-0.09460.39184.55589.845720.5945
121.71720.37561.10350.5462-0.33291.3992-0.1857-0.21180.07840.0280.1878-0.0644-0.3072-0.0285-0.02620.17390.0339-0.01770.28440.01950.1656.54856.2603-0.6971
133.77950.1793-0.75431.1276-0.50372.24970.0983-0.37280.21940.09850.0778-0.0754-0.15230.0466-0.00340.2006-0.028-0.02720.2414-0.00870.181917.89592.37960.1829
142.31880.72590.21694.372.00254.0408-0.0959-0.02020.27580.3078-0.0038-0.5736-0.209-0.06030.00960.2595-0.0324-0.02920.22050.0310.252225.7137.501-6.6393
151.776-0.09690.35892.56240.22221.2686-0.104-0.2170.25070.17480.00560.1514-0.2407-0.19270.06770.22770.0176-0.00130.2380.00030.198610.549413.0316-4.4917
162.23591.9191-0.89732.80530.67092.1746-0.0949-0.0880.76550.3158-0.10390.6603-0.5677-0.97070.2050.32590.1509-0.06310.3782-0.11230.3157-0.18117.5468-5.4502
171.5785-0.6621-0.2521.82981.14522.02580.05650.04580.06180.0718-0.165-0.1281-0.055-0.00120.16210.1845-0.0493-0.0040.17510.01080.134715.5835.4828-5.2186
180.3598-0.478-0.27040.7071-0.05064.10740.6136-0.42351.1179-0.8994-0.2301-0.117-0.25450.62820.14920.3202-0.08530.03930.30620.15790.512628.826714.3255-7.58
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 21 )
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 38 )
3X-RAY DIFFRACTION3chain 'A' and (resid 39 through 52 )
4X-RAY DIFFRACTION4chain 'A' and (resid 53 through 62 )
5X-RAY DIFFRACTION5chain 'A' and (resid 63 through 67 )
6X-RAY DIFFRACTION6chain 'A' and (resid 68 through 72 )
7X-RAY DIFFRACTION7chain 'A' and (resid 73 through 79 )
8X-RAY DIFFRACTION8chain 'A' and (resid 80 through 98 )
9X-RAY DIFFRACTION9chain 'A' and (resid 99 through 107 )
10X-RAY DIFFRACTION10chain 'A' and (resid 108 through 114 )
11X-RAY DIFFRACTION11chain 'A' and (resid 115 through 121 )
12X-RAY DIFFRACTION12chain 'B' and (resid 1 through 13 )
13X-RAY DIFFRACTION13chain 'B' and (resid 14 through 31 )
14X-RAY DIFFRACTION14chain 'B' and (resid 32 through 38 )
15X-RAY DIFFRACTION15chain 'B' and (resid 39 through 72 )
16X-RAY DIFFRACTION16chain 'B' and (resid 73 through 79 )
17X-RAY DIFFRACTION17chain 'B' and (resid 80 through 114 )
18X-RAY DIFFRACTION18chain 'B' and (resid 115 through 121 )

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