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- PDB-4yu7: Crystal structure of Piratoxin I (PrTX-I) complexed to caffeic acid -

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Basic information

Entry
Database: PDB / ID: 4yu7
TitleCrystal structure of Piratoxin I (PrTX-I) complexed to caffeic acid
ComponentsBasic phospholipase A2 homolog piratoxin-1
KeywordsTOXIN / Phospholipase A2 Phospholipase A2-like Bothrops snake venom inhibitor
Function / homology
Function and homology information


calcium-dependent phospholipase A2 activity / arachidonate secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / 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, 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
CAFFEIC ACID / Basic phospholipase A2 homolog piratoxin-1
Similarity search - Component
Biological speciesBothrops pirajai (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.647 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)2014/17864-8 Brazil
Citation
Journal: 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.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Crystallization and preliminary X-ray diffraction analysis of a Lys49-phospholipase A2 complexed with caffeic acid, a molecule with inhibitory properties against snake venoms.
Authors: Shimabuku, P.S. / Fernandes, C.A. / Magro, A.J. / Costa, T.R. / Soares, A.M. / Fontes, M.R.
History
DepositionMar 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Derived calculations
Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
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

Downloads & links

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Assembly

Deposited unit
B: Basic phospholipase A2 homolog piratoxin-1
A: Basic phospholipase A2 homolog piratoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,38810
Polymers27,5082
Non-polymers1,8808
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-11 kcal/mol
Surface area12720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.233, 72.082, 44.644
Angle α, β, γ (deg.)90.00, 102.08, 90.00
Int Tables number4
Space group name H-MP1211

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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-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#3: Chemical
ChemComp-DHC / CAFFEIC ACID / 3,4-DIHYDROXYCINNAMIC ACID


Mass: 180.157 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H8O4
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.1 / Details: PEG4000, Tris HCl pH 8.1, lithium sulfate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4568 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4568 Å / Relative weight: 1
ReflectionResolution: 1.6468→40 Å / Num. all: 27814 / Num. obs: 29444 / % possible obs: 94.47 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 27.4
Reflection shellResolution: 1.6468→1.706 Å / Num. measured obs: 2724

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IQ3

3iq3


Resolution: 1.647→37.341 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 24.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2287 1414 5.09 %
Rwork0.1823 --
obs0.1847 27807 94.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.647→37.341 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1849 0 108 289 2246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072004
X-RAY DIFFRACTIONf_angle_d1.1782659
X-RAY DIFFRACTIONf_dihedral_angle_d16.332765
X-RAY DIFFRACTIONf_chiral_restr0.079266
X-RAY DIFFRACTIONf_plane_restr0.006337
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6468-1.70560.31091300.27062588X-RAY DIFFRACTION92
1.7056-1.77390.32371420.26212637X-RAY DIFFRACTION95
1.7739-1.85460.29741470.22932684X-RAY DIFFRACTION96
1.8546-1.95240.25561450.19592699X-RAY DIFFRACTION96
1.9524-2.07470.24851440.18432682X-RAY DIFFRACTION97
2.0747-2.23490.24271530.16442695X-RAY DIFFRACTION97
2.2349-2.45980.21961160.17012711X-RAY DIFFRACTION96
2.4598-2.81560.23151490.18372649X-RAY DIFFRACTION94
2.8156-3.54690.21831400.17552619X-RAY DIFFRACTION94
3.5469-37.35060.19611480.17052429X-RAY DIFFRACTION86
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)
12.98250.59250.96923.37891.41923.0165-0.13350.22650.0079-0.28590.1087-0.1342-0.21690.0847-0.02780.17340.00840.01570.1986-0.00110.2223-8.5779-20.82546.0161
20.746-0.2991-0.99426.76551.99323.60890.12490.05940.1128-0.0890.262-0.3663-0.09680.5557-0.13680.21310.02070.00750.2962-0.03630.2428-0.2068-26.76456.6488
33.62841.7075-0.90192.9423-0.34392.6859-0.00120.26780.0557-0.25080.00490.23260.2061-0.2228-0.01480.24930.0073-0.02310.1996-0.02130.2249-7.7444-38.83319.2466
42.0238-1.08480.8232.4216-0.2981.66480.01920.1153-0.1374-0.12910.04840.3389-0.0328-0.263-0.05290.141-0.0071-0.01050.1999-0.01310.217-17.0014-29.51417.1644
55.8770.3421.5370.4561-0.38841.102-0.0388-0.31320.49120.0272-0.25460.4402-0.1182-0.38270.32150.14120.014-0.03030.2341-0.04210.2841-15.6001-13.472710.9792
66.638-3.02893.69292.5668-1.19512.9721-0.1185-0.2874-0.25450.090.14590.2314-0.1413-0.25680.00650.2008-0.01010.03170.1989-0.010.2241-13.5139-24.576712.8778
73.2869-0.767-0.39835.6440.84675.509-0.21850.2065-0.1243-0.2659-0.00240.03570.49210.28830.21590.20550.03880.04550.2054-0.01710.22870.2763-39.67578.3055
82.1546-1.80862.42098.0687-2.63722.8571-0.1508-0.1915-0.84980.45490.30811.14340.0928-0.7750.05080.4222-0.00630.12370.35540.02350.4791-15.5965-44.849812.0573
94.55270.7576-1.44922.7374-0.31652.787-0.14530.2081-0.23950.29110.0596-0.13120.24220.1084-0.0410.1306-0.014-0.00320.2003-0.0050.1927-3.3783-43.5782-9.3095
101.7546-0.79-0.57085.43071.91524.3712-0.039-0.5286-0.39420.22470.2644-0.34060.22630.1194-0.03530.18470.0046-0.04460.2747-0.02350.22393.3639-37.7388-4.8728
112.7876-0.32460.47952.2878-0.28971.885-0.0876-0.18360.34340.1990.06670.0981-0.2042-0.1841-0.00880.2535-0.0032-0.0060.1961-0.02180.2192-2.3946-25.894-10.1097
127.88561.81920.74373.5206-0.17452.6389-0.27310.27240.2362-0.24990.22930.3902-0.3054-0.39540.04320.16250.0202-0.02150.2167-0.00620.2236-6.2086-30.4954-16.0573
131.82990.5132-0.77793.59991.01473.3008-0.0092-0.22020.14290.40220.21810.4554-0.139-0.4549-0.26870.2485-0.05630.06560.4203-0.02980.3688-16.516-41.4193-10.5813
149.5316-2.25550.59751.1767-0.71271.09420.29450.5589-0.6604-0.1636-0.21420.4240.2673-0.28190.0090.1798-0.0128-0.02460.2525-0.0460.296-6.8553-50.6221-17.206
159.71912.4366-0.09911.64570.18710.9931-0.01450.21380.14470.02710.04330.18290.0647-0.1919-0.00210.17-0.02140.00010.25470.00190.2318-7.0024-40.752-17.5234
161.8405-0.0156-0.7944.32772.26335.4772-0.0974-0.59040.03570.45460.0592-0.2247-0.01670.80290.0410.1486-0.0458-0.06020.25760.00270.18088.7725-29.9771-10.439
173.6524-1.1143-0.19622.66920.81852.6185-0.3945-0.17550.32840.58470.17830.4862-0.55330.0758-0.06890.4451-0.0004-0.08580.1976-0.05910.33720.814-23.0517-3.3241
180.91170.8828-0.98885.0316-0.33811.1757-0.22660.35430.4116-0.2280.45240.724-0.69950.3530.15870.4238-0.0652-0.02440.30080.1250.4775-7.2558-19.3694-16.3493
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 13 )
2X-RAY DIFFRACTION2chain 'B' and (resid 14 through 21 )
3X-RAY DIFFRACTION3chain 'B' and (resid 22 through 38 )
4X-RAY DIFFRACTION4chain 'B' and (resid 39 through 65 )
5X-RAY DIFFRACTION5chain 'B' and (resid 66 through 79 )
6X-RAY DIFFRACTION6chain 'B' and (resid 80 through 102 )
7X-RAY DIFFRACTION7chain 'B' and (resid 103 through 114 )
8X-RAY DIFFRACTION8chain 'B' and (resid 115 through 121 )
9X-RAY DIFFRACTION9chain 'A' and (resid 1 through 13 )
10X-RAY DIFFRACTION10chain 'A' and (resid 14 through 21 )
11X-RAY DIFFRACTION11chain 'A' and (resid 22 through 38 )
12X-RAY DIFFRACTION12chain 'A' and (resid 39 through 53 )
13X-RAY DIFFRACTION13chain 'A' and (resid 54 through 65 )
14X-RAY DIFFRACTION14chain 'A' and (resid 66 through 79 )
15X-RAY DIFFRACTION15chain 'A' and (resid 80 through 98 )
16X-RAY DIFFRACTION16chain 'A' and (resid 99 through 107 )
17X-RAY DIFFRACTION17chain 'A' and (resid 108 through 114 )
18X-RAY DIFFRACTION18chain 'A' and (resid 115 through 121 )

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