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- PDB-6b84: Crystal structure of Myotoxin II from Bothrops moojeni -

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Basic information

Entry
Database: PDB / ID: 6b84
TitleCrystal structure of Myotoxin II from Bothrops moojeni
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
Basic phospholipase A2 homolog myotoxin II
Similarity search - Component
Biological speciesBothrops moojeni (Brazilian lancehead)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.997 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
B: Basic phospholipase A2 homolog 2
A: Basic phospholipase A2 homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4018
Polymers27,8242
Non-polymers5766
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-93 kcal/mol
Surface area11770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.848, 63.848, 126.366
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-310-

HOH

21B-346-

HOH

31A-354-

HOH

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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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.67 Å3/Da / Density % sol: 53.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 30% 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: 1.8→50 Å / Num. obs: 25137 / % possible obs: 99.7 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.047 / Rrim(I) all: 0.132 / Χ2: 0.935 / Net I/σ(I): 6.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.867.20.78124500.860.2960.8390.71599.2
1.86-1.947.30.58724370.8940.2220.6310.82499.2
1.94-2.037.30.40724980.9410.1550.4370.91499.8
2.03-2.137.30.33424560.960.1260.3580.99199.2
2.13-2.277.40.25425000.9720.0960.2731.00299.8
2.27-2.447.40.20924830.9780.080.2250.95799.8
2.44-2.697.60.16125140.9840.0610.1730.972100
2.69-3.087.70.11325320.9890.0430.1210.976100
3.08-3.887.90.08525700.9950.0320.0910.983100
3.88-507.60.07226970.9950.0280.0770.98999.6

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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: 1.997→27.43 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.81
RfactorNum. reflection% reflection
Rfree0.229 1049 5.03 %
Rwork0.1887 --
obs0.1907 20850 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.26 Å2 / Biso mean: 32.77 Å2 / Biso min: 17.63 Å2
Refinement stepCycle: final / Resolution: 1.997→27.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1904 0 30 222 2156
Biso mean--71.19 39.26 -
Num. residues----244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091976
X-RAY DIFFRACTIONf_angle_d1.2662640
X-RAY DIFFRACTIONf_chiral_restr0.044268
X-RAY DIFFRACTIONf_plane_restr0.005336
X-RAY DIFFRACTIONf_dihedral_angle_d12.713738
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9971-2.10240.29491430.21392730287399
2.1024-2.2340.25051450.202827922937100
2.234-2.40640.26561520.199228012953100
2.4064-2.64840.26161520.208628132965100
2.6484-3.03120.24321500.197928142964100
3.0312-3.81740.19261480.168928613009100
3.8174-27.43280.21531590.182829903149100
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)
10.0333-0.02870.04310.0157-0.04390.0510.22060.03210.02280.19710.0173-0.2522-0.0602-0.03980.00040.2705-0.0017-0.00990.2282-0.00630.216425.5408-16.22720.8113
20.07860.14950.03990.19190.09230.0888-0.05480.1291-0.3596-0.39830.222-0.0440.2036-0.22510.00040.3198-0.0063-0.0180.2276-0.0150.312413.6496-17.797419.7096
30.0789-0.02290.05360.0413-0.07840.10380.02810.1853-0.11270.0463-0.1174-0.0108-0.00850.0440.00010.258-0.00470.00390.1892-0.03560.225211.9299-7.227719.0966
40.20940.245-0.08870.60370.15720.13910.17410.03330.2238-0.0297-0.1667-0.2824-0.08770.42650.00040.2481-0.00230.03530.22060.02290.301330.6856-8.78818.2801
50.2442-0.4434-0.02110.81280.39570.60410.0242-0.16810.2735-0.0102-0.07510.2310.09110.03820.00010.24310.0023-0.00130.18090.00850.191216.5951-12.496122.9022
60.26680.0955-0.310.6364-0.06440.3271-0.30440.06210.866-0.36370.1207-0.4415-0.09130.0805-0.00350.29570.0518-0.08470.2985-0.0390.47534.3207-6.861513.7852
70.7216-0.02970.43280.27610.34581.02660.0287-0.04750.08170.02410.0227-0.1673-0.0520.11380.00010.2148-0.01740.00370.2102-0.03680.228.2464-26.94856.0869
81.082-0.4822-0.37550.25290.15920.19620.14160.00630.7452-0.016-0.1367-0.0305-0.5044-0.06970.02020.39440.0084-0.0180.28580.0120.3523-2.7612-17.63481.7977
91.5567-0.04050.40980.0573-0.02970.30850.1436-0.0839-0.1352-0.246-0.18710.34270.4532-0.16260.00240.268-0.0243-0.02910.257-0.02090.1868-8.8205-31.65433.0119
100.23290.0657-0.0810.43690.45850.48950.04970.1909-0.11550.06520.0429-0.08010.13110.1507-0.00010.24590.01160.00210.2412-0.02120.21945.5061-31.28823.9983
110.1192-0.15310.11360.1595-0.15410.122-0.09550.1226-0.08940.0819-0.1008-0.06820.25060.2952-0.03490.3428-0.06090.02830.3273-0.07310.311119.2784-22.42455.8523
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 52 )B32 - 52
4X-RAY DIFFRACTION4chain 'B' and (resid 53 through 79 )B53 - 79
5X-RAY DIFFRACTION5chain 'B' and (resid 80 through 112 )B80 - 112
6X-RAY DIFFRACTION6chain 'B' and (resid 113 through 122 )B113 - 122
7X-RAY DIFFRACTION7chain 'A' and (resid 1 through 53 )A1 - 53
8X-RAY DIFFRACTION8chain 'A' and (resid 54 through 65 )A54 - 65
9X-RAY DIFFRACTION9chain 'A' and (resid 66 through 79 )A66 - 79
10X-RAY DIFFRACTION10chain 'A' and (resid 80 through 107 )A80 - 107
11X-RAY DIFFRACTION11chain 'A' and (resid 108 through 122 )A108 - 122

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