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- PDB-6mqf: Myotoxin II from Bothrops moojeni complexed with Acetylsalicylic acid -

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Basic information

Entry
Database: PDB / ID: 6mqf
TitleMyotoxin II from Bothrops moojeni complexed with Acetylsalicylic acid
ComponentsBasic phospholipase A2 homolog 2
KeywordsTOXIN / Aspirin / Acetylsalicylic acid
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
2-(ACETYLOXY)BENZOIC ACID / Basic phospholipase A2 homolog myotoxin II
Similarity search - Component
Biological speciesBothrops moojeni (Brazilian lancehead)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.693 Å
AuthorsSalvador, G.H.M. / Fontes, M.R.M.
CitationJournal: Sci Rep / Year: 2019
Title: Search for efficient inhibitors of myotoxic activity induced by ophidian phospholipase A2-like proteins using functional, structural and bioinformatics approaches.
Authors: Salvador, G.H.M. / Cardoso, F.F. / Gomes, A.A. / Cavalcante, W.L.G. / Gallacci, M. / Fontes, M.R.M.
History
DepositionOct 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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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)28,4197
Polymers27,8242
Non-polymers5955
Water5,657314
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint1 kcal/mol
Surface area12460 Å2
2
A: Basic phospholipase A2 homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1713
Polymers13,9121
Non-polymers2582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Basic phospholipase A2 homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2494
Polymers13,9121
Non-polymers3363
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.553, 65.540, 55.121
Angle α, β, γ (deg.)90.000, 92.720, 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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-AIN / 2-(ACETYLOXY)BENZOIC ACID / ACETYLSALICYLIC ACID / ASPIRIN


Mass: 180.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H8O4 / Comment: antiinflammatory*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.56 Å3/Da / Density % sol: 52.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: PEG4000, Isopropanol, Sodium Citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 1.69→55.06 Å / Num. obs: 29583 / % possible obs: 94.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 18.47 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.032 / Rrim(I) all: 0.059 / Net I/σ(I): 16.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.69-1.783.10.3821279341040.8850.2570.4633.289.8
5.35-55.063.40.04233099810.9790.0270.0530.595.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.69 Å55.06 Å
Translation1.69 Å55.06 Å

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHASER2.8.0phasing
PHENIX1.12refinement
PDB_EXTRACT3.24data extraction
autoPROC1.0.5data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6B80

6b80


Resolution: 1.693→18.884 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.24
RfactorNum. reflection% reflection
Rfree0.2183 1441 4.88 %
Rwork0.1786 --
obs0.1805 29545 94.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 75.18 Å2 / Biso mean: 25.2438 Å2 / Biso min: 9.5 Å2
Refinement stepCycle: final / Resolution: 1.693→18.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1908 0 38 314 2260
Biso mean--39.1 33.77 -
Num. residues----244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131995
X-RAY DIFFRACTIONf_angle_d1.2162683
X-RAY DIFFRACTIONf_chiral_restr0.065268
X-RAY DIFFRACTIONf_plane_restr0.008342
X-RAY DIFFRACTIONf_dihedral_angle_d16.9461198
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 (%)
1.6931-1.75360.28921290.23692634276389
1.7536-1.82380.27431350.232759289492
1.8238-1.90670.22561500.18612749289993
1.9067-2.00710.25271410.20262762290393
2.0071-2.13270.25771550.17622806296195
2.1327-2.29710.22781390.19322827296694
2.2971-2.52780.24541440.17982873301796
2.5278-2.89240.21781560.17772877303396
2.8924-3.63990.19191450.16782889303496
3.6399-18.88530.18481470.162928307596
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)
11.33820.4393-0.46950.9947-0.32431.5038-0.0685-0.0115-0.02760.02540.0051-0.1512-0.0221-0.00320.0520.08210.0041-0.01870.12910.00140.138710.826-73.36150.748
21.0535-0.0712-0.55170.4350.27420.5429-0.12080.0283-0.1114-0.1592-0.0688-0.345-0.2370.30880.11780.1749-0.0158-0.00870.22220.0460.210318.401-65.91436.597
30.73330.6665-0.19230.76730.07451.2806-0.15680.1227-0.055-0.01560.0514-0.01540.1154-0.16790.05760.07840.0070.00390.14150.00760.14486.456-76.42150.26
41.1957-0.0863-0.08952.0195-0.74752.2273-0.0355-0.0489-0.05940.313-0.0501-0.0409-0.3809-0.00410.04360.1871-0.013-0.00360.1346-0.00110.11046.985-73.34674.965
51.3267-0.1513-1.82440.42250.84494.1997-0.29220.0654-0.09670.3319-0.0214-0.05920.5589-0.0080.11220.30530.05630.0510.14760.01870.21559.492-86.66783.281
61.2651-0.30030.06882.4257-0.1411.9404-0.0668-0.0630.1290.7395-0.0544-0.073-0.4441-0.0068-0.01150.34520.00020.01730.1514-0.01590.12586.637-73.36980.802
72.0127-0.56850.0072.18210.14392.44330.0598-0.0959-0.02790.3208-0.1719-0.1565-0.6120.12880.15230.2488-0.0677-0.03780.1860.03240.17411.519-66.21565.756
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:61 )A1 - 61
2X-RAY DIFFRACTION2( CHAIN A AND RESID 67:79 )A67 - 79
3X-RAY DIFFRACTION3( CHAIN A AND RESID 80:122 )A80 - 122
4X-RAY DIFFRACTION4( CHAIN B AND RESID 1:53 )B1 - 53
5X-RAY DIFFRACTION5( CHAIN B AND RESID 57:79 )B57 - 79
6X-RAY DIFFRACTION6( CHAIN B AND RESID 80:107 )B80 - 107
7X-RAY DIFFRACTION7( CHAIN B AND RESID 108:122 )B108 - 122

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