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- PDB-6pwh: Cystal structure of Myotoxin II from Bothrops moojeni co-crystall... -

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Basic information

Entry
Database: PDB / ID: 6pwh
TitleCystal structure of Myotoxin II from Bothrops moojeni co-crystallized with Varespladib (LY315920)
ComponentsBasic phospholipase A2 homolog 2
KeywordsTOXIN / Myotoxin II / MjTX-II / Lys49-PLA2 / Varespladib
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
Chem-VRD / Basic phospholipase A2 homolog myotoxin II
Similarity search - Component
Biological speciesBothrops moojeni (Brazilian lancehead)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.749 Å
AuthorsSalvador, G.H.M. / Fontes, M.R.M.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2015/24167-7 Brazil
CitationJournal: Sci Rep / Year: 2019
Title: Structural basis for phospholipase A2-like toxin inhibition by the synthetic compound Varespladib (LY315920).
Authors: Salvador, G.H.M. / Gomes, A.A.S. / Bryan-Quiros, W. / Fernandez, J. / Lewin, M.R. / Gutierrez, J.M. / Lomonte, B. / Fontes, M.R.M.
History
DepositionJul 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.2Oct 11, 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)28,7416
Polymers27,8242
Non-polymers9174
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-14 kcal/mol
Surface area12200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.864, 37.189, 68.681
Angle α, β, γ (deg.)90.000, 114.390, 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) / Tissue: Venom Gland / References: UniProt: Q9I834
#2: Chemical ChemComp-VRD / ({3-[amino(oxo)acetyl]-1-benzyl-2-ethyl-1H-indol-4-yl}oxy)acetic acid / Varespladib


Mass: 380.394 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H20N2O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: antiinflammatory, inhibitor*YM
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.29 Å3/Da / Density % sol: 46.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% v/w PEG4000, 0.1M Tris HCl, 0.2M Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.425 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 1, 2017 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.425 Å / Relative weight: 1
ReflectionResolution: 1.749→40 Å / Num. obs: 25514 / % possible obs: 98.6 % / Redundancy: 4.4 % / Biso Wilson estimate: 34.48 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.039 / Rrim(I) all: 0.082 / Χ2: 1.026 / Net I/σ(I): 9.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.75-1.813.80.42224400.9320.2380.4870.94894.9
1.81-1.894.40.31325400.9520.1650.3560.99898.2
1.89-1.974.70.25825060.9670.1320.2911.05498.4
1.97-2.074.60.17125360.9780.090.1941.05599.1
2.07-2.24.50.12525700.9850.0670.1421.07299.2
2.2-2.384.10.10225470.9890.0570.1181.04899.5
2.38-2.614.60.08725740.9920.0460.0981.04599.8
2.61-2.994.70.08125850.9930.0420.0911.01699.9
2.99-3.774.40.07225830.9920.0390.0831.01299.2
3.77-404.10.06226330.9940.0340.0710.99497.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.75 Å33.44 Å
Translation1.75 Å33.44 Å

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Processing

Software
NameVersionClassification
HKL-20001.8.4data reduction
SCALEPACKdata scaling
PHASER2.7.16phasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KF3

4kf3


Resolution: 1.749→33.438 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.87
RfactorNum. reflection% reflection
Rfree0.2323 1254 4.92 %
Rwork0.2122 --
obs0.2132 25477 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 141.87 Å2 / Biso mean: 57.037 Å2 / Biso min: 23.82 Å2
Refinement stepCycle: final / Resolution: 1.749→33.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1879 0 64 93 2036
Biso mean--48.75 51.83 -
Num. residues----244
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7493-1.81930.29171340.2906256595
1.8193-1.90210.30061350.2645267198
1.9021-2.00240.29871390.2686266599
2.0024-2.12780.26041400.2491266799
2.1278-2.29210.24311420.2392273299
2.2921-2.52260.23061400.23062698100
2.5226-2.88750.30721450.22592740100
2.8875-3.63720.2451380.2051271299
3.6372-33.4380.18421410.1874277398
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)
18.00891.424-0.69434.7295-1.58714.0006-0.04880.3223-0.09490.07280.0154-0.577-0.1686-0.0388-0.03270.27180.03390.00330.2184-0.0550.204-4.9467-3.261475.7691
24.7051-0.63094.30384.7316-4.48297.37020.05641.61920.669-0.2131-0.0703-0.5551-0.25340.91970.00770.5016-0.04530.23020.75480.10490.89239.35941.966767.305
38.02040.90090.06092.8729-2.41833.60890.2216-0.3599-0.63460.1925-0.2586-0.6509-0.06130.16020.04460.30750.00680.0050.2191-0.04520.3402-4.5655-6.888279.5783
48.50660.4459-0.28584.35590.13714.17540.05260.69670.0782-0.0868-0.09560.3991-0.18-0.36190.03370.2881-0.0095-0.02960.59670.10260.3754-29.249-5.588177.63
56.56681.85242.99413.5311.18821.40060.8089-3.57610.1221.26690.0063-0.0058-0.2479-0.002-0.04250.7144-0.1780.09091.528-0.43230.4739-37.82-0.991589.9358
69.29730.382-0.94681.2735-1.58844.06040.27221.30050.4191-0.27850.01380.4653-0.1029-0.5906-0.30060.3385-0.0107-0.02340.7517-0.01420.4434-29.8594-4.810974.4746
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 74 )A1 - 74
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 88 )A75 - 88
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 133 )A89 - 133
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 57 )B1 - 57
5X-RAY DIFFRACTION5chain 'B' and (resid 58 through 88 )B58 - 88
6X-RAY DIFFRACTION6chain 'B' and (resid 89 through 133 )B89 - 133

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