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- PDB-6b81: Crystal structure of Myotoxin II from Bothrops moojeni complexed ... -

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Basic information

Entry
Database: PDB / ID: 6b81
TitleCrystal structure of Myotoxin II from Bothrops moojeni complexed to Caprylic acid
ComponentsBasic phospholipase A2 homolog 2
KeywordsTOXIN / Myotoxin II / Bothrops moojeni / Phospholipase A2-like
Function / homology
Function and homology information


calcium-dependent phospholipase A2 activity / arachidonate 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 / arachidonate 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
OCTANOIC ACID (CAPRYLIC ACID) / Basic phospholipase A2 homolog myotoxin II
Similarity search - Component
Biological speciesBothrops moojeni (Brazilian lancehead)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 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)28,68910
Polymers27,8242
Non-polymers8658
Water6,738374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-91 kcal/mol
Surface area11870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.061, 61.683, 54.027
Angle α, β, γ (deg.)90.000, 118.930, 90.000
Int Tables number4
Space group name H-MP1211

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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


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-OCA / OCTANOIC ACID (CAPRYLIC ACID)


Mass: 144.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.68 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 32% 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.425 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 28293 / % possible obs: 96.2 % / Redundancy: 3 % / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.073 / Rrim(I) all: 0.13 / Χ2: 0.953 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.76-1.8230.55729420.6850.3830.680.74999.9
1.82-1.930.42529120.7580.290.5180.783100
1.9-1.9830.31928620.8470.2180.3880.83198.2
1.98-2.0930.25327750.8780.1740.3090.92695.8
2.09-2.2230.18828050.9310.1290.231.02694.6
2.22-2.3930.16627110.9380.1160.2031.05293.2
2.39-2.632.90.14227080.9510.1010.1751.09492.1
2.63-3.012.90.11327830.9720.080.1391.04294
3.01-3.7930.07129180.9920.0470.0861.06798.9
3.79-503.10.05828770.9930.0380.070.98595.2

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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: 1.76→26.671 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.35
RfactorNum. reflection% reflection
Rfree0.2016 1405 4.97 %
Rwork0.173 --
obs0.1744 28283 96.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 67.06 Å2 / Biso mean: 20.88 Å2 / Biso min: 7.42 Å2
Refinement stepCycle: final / Resolution: 1.76→26.671 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1916 0 50 374 2340
Biso mean--28.49 31.15 -
Num. residues----244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052002
X-RAY DIFFRACTIONf_angle_d0.9552662
X-RAY DIFFRACTIONf_chiral_restr0.039268
X-RAY DIFFRACTIONf_plane_restr0.005338
X-RAY DIFFRACTIONf_dihedral_angle_d14.183768
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7555-1.81820.27941360.22582759289599
1.8182-1.8910.21721530.201127572910100
1.891-1.9770.21561520.17692719287198
1.977-2.08120.19381410.17412652279396
2.0812-2.21160.19781380.16732667280595
2.2116-2.38220.20021200.17632603272393
2.3822-2.62180.22591340.18312567270192
2.6218-3.00070.20841530.17612634278794
3.0007-3.77890.17961370.16852783292099
3.7789-26.67390.19171410.1562737287895
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)
10.37360.1381-0.19680.0714-0.11140.2672-0.0164-0.13280.08840.0513-0.0370.0716-0.21180.16870.01530.08190.0028-0.00560.10510.01970.09660.90928.907723.4079
20.0311-0.0252-0.03170.0494-0.03330.0652-0.03840.06810.0190.1490.0470.02050.09020.087400.09940.00510.00680.13040.00950.15265.2542-1.687725.1089
30.2253-0.0743-0.25060.30490.17290.2751-0.09080.1252-0.061-0.128-0.00610.06190.0409-0.0219-0.00550.1319-0.0165-0.01690.12310.00610.1466-5.7242-1.172717.7413
40.27420.0989-0.20730.0946-0.1350.3260.0875-0.01340.0893-0.2181-0.09440.2554-0.2459-0.04160.03060.13750.0208-0.03050.10250.0080.1226-6.777916.479925.0546
50.36570.2621-0.23620.46170.10670.3021-0.0632-0.0531-0.01020.10440.03020.0789-0.06530.042-0.02020.09590.00290.01340.10960.00630.0913-4.55761.871426.1443
60.2145-0.13220.07380.2858-0.16760.1042-0.0738-0.25270.26050.0626-0.07070.16430.0199-0.05970.02510.06510.00370.02010.0874-0.01160.13436.8037-12.129919.7577
70.0872-0.02430.02280.0098-0.00980.0548-0.1881-0.0091-0.1372-0.08550.0706-0.2393-0.09520.0394-0.01080.1563-0.04320.01550.1715-0.03320.2353-9.6093-13.549616.9424
80.0511-0.0231-0.0034-0.00930.00180.01340.0776-0.0142-0.2573-0.00650.0636-0.01390.16390.0720.00120.0865-0.004-0.00320.11580.0040.101814.799-14.297512.2083
90.0147-0.0242-0.01120.02620.01620.0064-0.0338-0.2622-0.12930.01150.1359-0.0512-0.00840.06310.00020.1221-0.00070.02130.1350.00830.134616.747-7.115518.5347
100.3289-0.1094-0.07820.08450.0340.08340.25290.14340.2155-0.4205-0.07320.0272-0.0031-0.07320.05270.2210.0264-0.00280.15040.02480.138513.63410.60266.2484
110.10.1842-0.20590.309-0.35920.42780.03120.09090.12720.2573-0.06620.3888-0.3402-0.12310.02290.2195-0.0003-0.06170.2154-0.02460.23524.4438-14.32153.3784
120.0089-0.00620.00470.0261-0.02110.0176-0.03940.118-0.2676-0.170.1230.01090.12730.0746-0.00020.14110.0110.00770.1977-0.00690.140421.8705-22.1718.3714
130.88970.35230.38920.2010.41951.23550.08180.04450.0405-0.13930.16560.0387-0.01730.06020.40640.1781-0.0037-0.1052-0.0288-0.1439-0.004813.2074-21.63430.2927
140.3716-0.1844-0.05770.93370.11030.36620.1045-0.00150.0677-0.3456-0.0538-0.1471-0.14290.0410.06230.12380.00530.00360.1517-0.01130.102618.7195-7.26067.5157
150.16010.02450.14430.17950.12360.22050.18420.0651-0.0354-0.1429-0.0374-0.12460.05210.330.09550.13380.01220.01780.11740.01790.12179.97316.77417.244
160.08760.03090.07480.05040.00660.06710.21510.0317-0.0177-0.1837-0.00690.07090.0552-0.03740.15160.58030.1970.0233-0.06620.19230.035510.69188.20160.6029
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 15 through 27 )B15 - 27
3X-RAY DIFFRACTION3chain 'B' and (resid 28 through 74 )B28 - 74
4X-RAY DIFFRACTION4chain 'B' and (resid 75 through 88 )B75 - 88
5X-RAY DIFFRACTION5chain 'B' and (resid 89 through 117 )B89 - 117
6X-RAY DIFFRACTION6chain 'B' and (resid 118 through 126 )B118 - 126
7X-RAY DIFFRACTION7chain 'B' and (resid 127 through 133 )B127 - 133
8X-RAY DIFFRACTION8chain 'A' and (resid 1 through 13 )A1 - 13
9X-RAY DIFFRACTION9chain 'A' and (resid 15 through 22 )A15 - 22
10X-RAY DIFFRACTION10chain 'A' and (resid 23 through 57 )A23 - 57
11X-RAY DIFFRACTION11chain 'A' and (resid 58 through 74 )A58 - 74
12X-RAY DIFFRACTION12chain 'A' and (resid 75 through 81 )A75 - 81
13X-RAY DIFFRACTION13chain 'A' and (resid 82 through 88 )A82 - 88
14X-RAY DIFFRACTION14chain 'A' and (resid 89 through 117 )A89 - 117
15X-RAY DIFFRACTION15chain 'A' and (resid 118 through 126 )A118 - 126
16X-RAY DIFFRACTION16chain 'A' and (resid 127 through 133 )A127 - 133

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