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- PDB-6b83: Crystal structure of Myotoxin II from Bothrops moojeni complexed ... -

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Basic information

Entry
Database: PDB / ID: 6b83
TitleCrystal structure of Myotoxin II from Bothrops moojeni complexed to Caproic acid
ComponentsBasic phospholipase A2 homolog 2
KeywordsTOXIN / Myotoxin II / Bothrops moojeni / Phospholipase A2-like
Function / homology
Function and homology information


phospholipase A2 activity / arachidonic acid secretion / defense response to fungus / phospholipid metabolic process / lipid catabolic process / 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
HEXANOIC ACID / Basic phospholipase A2 homolog myotoxin II
Similarity search - Component
Biological speciesBothrops moojeni (Brazilian lancehead)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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

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Assembly

Deposited unit
B: Basic phospholipase A2 homolog 2
A: Basic phospholipase A2 homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,46110
Polymers27,6722
Non-polymers7898
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-100 kcal/mol
Surface area12670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.238, 62.991, 88.106
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: 13836.114 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bothrops moojeni (Brazilian lancehead) / References: UniProt: Q9I834
#2: Chemical ChemComp-6NA / HEXANOIC ACID / Caproic acid


Mass: 116.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O2
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 24% PEG4000, 0.1 M Tris HCl, 0.2 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: 1.7→40 Å / Num. obs: 31375 / % possible obs: 97.5 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.025 / Rrim(I) all: 0.057 / Χ2: 0.986 / Net I/σ(I): 17.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.784.60.39638720.9120.2010.4460.84598.2
1.78-1.874.60.23739160.9660.1210.2681.01499
1.87-1.994.70.15539190.9810.0780.1741.06398.8
1.99-2.144.70.139580.9890.050.1121.01499.4
2.14-2.364.80.07639620.9930.0380.0850.99299.4
2.36-2.74.80.0639720.9950.0290.0671.02998.6
2.7-3.44.90.04839280.9970.0230.0540.91296.7
3.4-4050.0438480.9980.0190.0451.01390.6

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
Coot0.8.6model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KF3

4kf3


Resolution: 1.7→26.832 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.75
RfactorNum. reflection% reflection
Rfree0.2051 1568 5 %
Rwork0.1887 --
obs0.1895 31342 97.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 121.07 Å2 / Biso mean: 37.9 Å2 / Biso min: 16.03 Å2
Refinement stepCycle: final / Resolution: 1.7→26.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1890 0 43 304 2237
Biso mean--69.87 41.13 -
Num. residues----244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031978
X-RAY DIFFRACTIONf_angle_d0.9462640
X-RAY DIFFRACTIONf_chiral_restr0.036268
X-RAY DIFFRACTIONf_plane_restr0.003334
X-RAY DIFFRACTIONf_dihedral_angle_d12.417743
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6993-1.75420.28871410.26582677281898
1.7542-1.81680.22941410.22812687282899
1.8168-1.88960.22931430.20252708285199
1.8896-1.97550.23651420.20632707284999
1.9755-2.07970.24941440.196727202864100
2.0797-2.20990.19221430.197227412884100
2.2099-2.38040.21531440.18772728287299
2.3804-2.61980.21251450.1912752289799
2.6198-2.99850.2671430.19682722286598
2.9985-3.77610.18571420.17682686282896
3.7761-26.8350.1671400.17552646278690
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)
13.20450.26730.03793.26770.95014.1294-0.21010.10850.0409-0.47320.5516-0.313-0.19530.7815-0.30830.2412-0.07780.0380.3492-0.05540.212813.91767.8-23.0854
22.6832-0.8056-2.22744.83280.8882.4644-0.25790.5268-0.3828-0.26920.8903-0.87990.09280.7735-0.51330.19410.01580.01930.4393-0.15190.353117.1644-3.9822-22.1326
32.8945-0.45960.12823.3040.42152.1857-0.23290.1834-0.1895-0.33430.28870.4322-0.01540.0606-0.11190.2347-0.0365-0.05250.223-0.03720.27956.2952-7.2719-23.9767
41.69110.030.15332.24121.35473.8589-0.15320.3950.0038-0.85240.310.2061-0.07320.1386-0.17940.5007-0.0793-0.04480.25720.03530.17577.49910.949-27.3814
50.3506-0.09450.51250.0301-0.22434.5184-0.38750.39210.3694-1.290.17890.9542-0.8787-1.0152-0.08750.682-0.0067-0.23410.37740.08690.39122.39514.6517-27.3313
62.45270.04560.50974.5684-0.5685.5986-0.1150.1845-0.0204-0.56840.38770.6544-0.2064-0.1516-0.32380.2499-0.04-0.05710.1947-0.00160.2814.48155.361-23.3332
76.2356-2.73280.49327.6302-3.2214.08070.41530.0985-0.86320.4740.0471-0.31060.94861.1683-0.21490.30250.1813-0.16110.3781-0.13980.367915.987-7.7154-12.8619
84.5552-2.5224-0.6771.39640.45180.3698-0.2132-0.3723-0.49840.09510.447-0.36490.4530.90670.09770.49660.09590.13030.6593-0.05480.680719.7971-12.3436-24.3967
96.4272-2.00081.30692.7092-0.66861.0764-0.24290.502-0.4337-0.4190.397-0.1611-0.00550.2771-0.14160.2823-0.02090.0030.272-0.08040.42473.5086-15.2657-27.7668
104.63790.29281.56771.47940.33743.72350.1227-0.71220.16790.1298-0.0781-0.03070.3276-0.26860.02940.1982-0.01830.02170.3465-0.05910.201728.6215-14.2308-33.287
112.4853-1.1001-1.67813.50290.63611.21630.1059-1.03190.10740.4049-0.04980.528-0.18250.1663-0.00060.22480.00580.03850.5134-0.13340.354430.7825-7.2198-26.3926
122.0531-0.00521.06742.0049-0.3652.67890.1425-0.12880.7135-0.3999-0.00170.1949-0.974-0.0602-0.13520.43910.02860.03190.2878-0.13990.498928.89933.654-35.2292
130.25440.0943-0.05511.20690.88933.9004-0.09090.26410.4079-0.64930.1664-0.1389-0.65610.3872-0.06560.35760.00260.01360.2127-0.02820.347229.8749-1.652-42.0779
143.8649-0.4174-0.18712.3885-0.05873.841-0.1266-0.2707-0.05610.10830.0490.2549-0.3626-0.55490.14540.21050.013-0.02570.2699-0.01860.204119.2357-13.1369-42.9578
154.9466-0.66843.10451.5493-0.25523.81760.1820.1288-0.3657-0.1963-0.06620.04670.3652-0.0016-0.03760.21980.0008-0.00770.2144-0.01040.235832.1874-21.9115-40.6594
163.52780.27340.4052.53931.42672.73540.0502-0.18280.1599-0.18310.0634-0.2833-0.25950.2186-0.14720.1808-0.00290.03740.2356-0.01690.237533.0863-10.2791-40.3415
174.9831-1.761-0.22912.75241.33252.8981-0.3571-1.30670.47480.4490.3228-0.4404-0.6790.5588-0.23520.4185-0.0763-0.02160.5296-0.25680.481735.91233.4428-26.3379
186.7206-1.19291.21796.1159-3.62098.08650.5385-1.04861.5231-0.46570.78790.7823-1.5521-0.80430.12781.0373-0.1530.33760.943-0.17460.830425.85966.3011-27.4721
192.78920.74712.69123.92811.00122.641-0.0066-0.03041.1045-0.81810.38460.4083-0.39880.1609-0.63730.901-0.0090.07840.2933-0.04310.80827.91558.8258-44.3842
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 13 )B1 - 13
2X-RAY DIFFRACTION2chain 'B' and (resid 14 through 31 )B14 - 31
3X-RAY DIFFRACTION3chain 'B' and (resid 32 through 53 )B32 - 53
4X-RAY DIFFRACTION4chain 'B' and (resid 54 through 72 )B54 - 72
5X-RAY DIFFRACTION5chain 'B' and (resid 73 through 79 )B73 - 79
6X-RAY DIFFRACTION6chain 'B' and (resid 80 through 98 )B80 - 98
7X-RAY DIFFRACTION7chain 'B' and (resid 99 through 107 )B99 - 107
8X-RAY DIFFRACTION8chain 'B' and (resid 108 through 115 )B108 - 115
9X-RAY DIFFRACTION9chain 'B' and (resid 116 through 122 )B116 - 122
10X-RAY DIFFRACTION10chain 'A' and (resid 1 through 13 )A1 - 13
11X-RAY DIFFRACTION11chain 'A' and (resid 14 through 21 )A14 - 21
12X-RAY DIFFRACTION12chain 'A' and (resid 22 through 38 )A22 - 38
13X-RAY DIFFRACTION13chain 'A' and (resid 39 through 53 )A39 - 53
14X-RAY DIFFRACTION14chain 'A' and (resid 54 through 65 )A54 - 65
15X-RAY DIFFRACTION15chain 'A' and (resid 66 through 79 )A66 - 79
16X-RAY DIFFRACTION16chain 'A' and (resid 80 through 102 )A80 - 102
17X-RAY DIFFRACTION17chain 'A' and (resid 103 through 107 )A103 - 107
18X-RAY DIFFRACTION18chain 'A' and (resid 108 through 115 )A108 - 115
19X-RAY DIFFRACTION19chain 'A' and (resid 116 through 122 )A116 - 122

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