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- PDB-6b80: Crystal structure of myotoxin II from Bothrops moojeni complexed ... -

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Basic information

Entry
Database: PDB / ID: 6b80
TitleCrystal structure of myotoxin II from Bothrops moojeni complexed to myristic acid
ComponentsBasic phospholipase A2 homolog 2
KeywordsTOXIN / Myotoxin II / Phospholipase A2-like / Bothrops moojeni
Function / homology
Function and homology information


calcium-dependent phospholipase A2 activity / arachidonic acid secretion / defense response to fungus / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / phospholipid binding / toxin activity / killing of cells of another organism / defense response to bacterium ...calcium-dependent phospholipase A2 activity / arachidonic acid secretion / defense response to fungus / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / phospholipid binding / toxin activity / killing of cells of another organism / defense response to bacterium / 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
MYRISTIC ACID / Basic phospholipase A2 homolog myotoxin II
Similarity search - Component
Biological speciesBothrops moojeni (Brazilian lancehead)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.949 Å
AuthorsSalvador, G.H.M. / dos Santos, J.I. / Fontes, M.R.M.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2015/24167-7 Brazil
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2018
Title: Structural evidence for a fatty acid-independent myotoxic mechanism for a phospholipase A2-like toxin.
Authors: Salvador, G.H.M. / Dos Santos, J.I. / Borges, R.J. / Fontes, M.R.M.
History
DepositionOct 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
A: Basic phospholipase A2 homolog 2
B: Basic phospholipase A2 homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,21211
Polymers27,8242
Non-polymers1,3889
Water5,639313
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-91 kcal/mol
Surface area12140 Å2
Unit cell
Length a, b, c (Å)50.545, 62.795, 86.848
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Basic phospholipase A2 homolog 2 / svPLA2 homolog / M-VI / MjTX-II / Myotoxin II


Mass: 13912.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bothrops moojeni (Brazilian lancehead) / Organ: Venom gland / References: UniProt: Q9I834
#2: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: 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.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.48 Å3/Da / Density % sol: 50.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG4000, 0.1 M Tris HCl, 0.25 M Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.425 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 25, 2014 / Details: mirrors
RadiationMonochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.425 Å / Relative weight: 1
ReflectionResolution: 1.949→40 Å / Num. obs: 20141 / % possible obs: 96.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.172 / Χ2: 1.214 / Net I/σ(I): 5.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.949-2.045.30.67824041.353194.4
2.04-2.155.40.50923981.416194.3
2.15-2.285.30.37624201.185194.5
2.28-2.465.30.29624471.164195.2
2.46-2.75.20.23325191.1197.5
2.7-3.15.30.17125761.156198.7
3.1-3.95.50.13226041.321199.2
3.9-405.40.10227731.041199.7

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
Coot0.8.6model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KF3

4kf3


Resolution: 1.949→35.861 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.33
RfactorNum. reflection% reflection
Rfree0.1983 1999 9.95 %
Rwork0.1698 --
obs0.1726 20097 96.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.08 Å2 / Biso mean: 22.8888 Å2 / Biso min: 10.97 Å2
Refinement stepCycle: final / Resolution: 1.949→35.861 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1900 0 86 313 2299
Biso mean--30.93 30.83 -
Num. residues----244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012029
X-RAY DIFFRACTIONf_angle_d1.3762691
X-RAY DIFFRACTIONf_chiral_restr0.083268
X-RAY DIFFRACTIONf_plane_restr0.006337
X-RAY DIFFRACTIONf_dihedral_angle_d15.977786
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9489-1.99760.28141330.26971195132892
1.9976-2.05160.2691370.21991248138594
2.0516-2.1120.2191370.19121248138594
2.112-2.18010.21581390.18041246138594
2.1801-2.2580.21411340.17731217135194
2.258-2.34840.25471400.18311267140795
2.3484-2.45530.20551400.17841265140596
2.4553-2.58470.20021430.18011294143797
2.5847-2.74660.191430.17421293143698
2.7466-2.95860.21671470.17651340148799
2.9586-3.25610.22221460.15781319146599
3.2561-3.72690.17251500.15711345149599
3.7269-4.69380.14441510.132613671518100
4.6938-35.8670.19151590.172714541613100
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)
11.9834-0.73120.63631.54890.44861.2769-0.0113-0.0394-0.0890.01120.051-0.03010.1437-0.0572-0.02590.1295-0.00220.01560.13960.01360.125721.933167.963398.0394
24.16241.114-2.49854.177-1.45446.27590.07990.13030.0339-0.32470.01410.0570.3934-0.085-0.09470.1780.0193-0.01730.156-0.02730.171421.018164.137289.2182
30.6553-0.79990.79141.3389-1.27921.2621-0.11380.0764-0.0106-0.0270.0907-0.10140.21930.41390.04940.12520.00080.02310.2259-0.00540.198131.38775.252287.2243
45.1779-0.4009-2.99451.56290.49843.96780.14760.30670.2153-0.1912-0.0518-0.0288-0.2154-0.098-0.05250.14840.0116-0.00840.1677-0.00270.168418.957984.579190.6666
53.20381.6872-1.17852.6122-1.2732.0872-0.1120.2943-0.1384-0.20140.07180.12710.1676-0.19130.00450.10040.0141-0.02020.1296-0.02630.145718.091272.994790.376
62.03230.66972.60686.3149-2.34668.97430.3076-0.0178-0.75740.3352-0.04550.24020.3516-0.28-0.07690.1932-0.02890.020.22040.01090.322215.253659.2368104.1604
70.25830.1850.17924.37360.9744.82790.05090.0301-0.15390.05060.15760.04440.59660.1635-0.11230.20320.0107-0.0060.16480.00620.240124.774555.250496.0587
81.50090.1186-0.18972.4733-0.35570.4268-0.0705-0.0009-0.03850.03140.07740.0693-0.026-0.0132-0.01220.14050.0013-0.00920.1740.0210.12636.405664.546108.2284
94.34290.0733-1.67883.8679-0.76993.5525-0.17460.0075-0.0021-0.0883-0.0579-0.2864-0.03920.1122-0.02410.1453-0.02410.02090.13820.02180.158545.737567.655106.0041
101.23610.6156-0.81862.6373-2.62616.6543-0.08540.18180.0651-0.68020.0111-0.06620.41990.34740.2460.2755-0.00720.01890.1682-0.02250.151643.97351.1829103.2288
112.3573-0.5893-0.83762.63031.50144.7749-0.00410.11740.0767-0.17370.1982-0.40380.01790.2618-0.05340.1653-0.02-0.00740.13320.0370.228546.03257.6102107.2183
122.43570.35630.42431.2352-0.50561.0429-0.1480.05330.42150.11860.1316-0.0762-0.1613-0.1476-0.00870.16540.0213-0.01320.12-0.01780.221136.57874.6591109.8338
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 39 )A1 - 39
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 53 )A40 - 53
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 74 )A57 - 74
4X-RAY DIFFRACTION4chain 'A' and (resid 75 through 88 )A75 - 88
5X-RAY DIFFRACTION5chain 'A' and (resid 89 through 112 )A89 - 112
6X-RAY DIFFRACTION6chain 'A' and (resid 113 through 117 )A113 - 117
7X-RAY DIFFRACTION7chain 'A' and (resid 118 through 133 )A118 - 133
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 39 )B1 - 39
9X-RAY DIFFRACTION9chain 'B' and (resid 40 through 57 )B40 - 57
10X-RAY DIFFRACTION10chain 'B' and (resid 58 through 88 )B58 - 88
11X-RAY DIFFRACTION11chain 'B' and (resid 89 through 108 )B89 - 108
12X-RAY DIFFRACTION12chain 'B' and (resid 109 through 133 )B109 - 133

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