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- PDB-7lye: Myotoxin I from Bothrops moojeni co-crystallized with synthetic i... -

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Basic information

Entry
Database: PDB / ID: 7lye
TitleMyotoxin I from Bothrops moojeni co-crystallized with synthetic inhibitor Varespladib (LY315920)
ComponentsBasic phospholipase A2 homolog BomoTx
KeywordsTOXIN / Myotoxin I / MjTX-I / PLA2-like
Function / homology
Function and homology information


calcium-dependent phospholipase A2 activity / arachidonate secretion / lipid catabolic process / negative regulation of T cell proliferation / phospholipid metabolic process / phospholipid binding / toxin activity / calcium ion binding / extracellular region
Similarity search - Function
Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 domain superfamily
Similarity search - Domain/homology
Chem-VRD / Basic phospholipase A2 homolog MjTX-I
Similarity search - Component
Biological speciesBothrops moojeni (Brazilian lancehead)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.758 Å
AuthorsSalvador, G.H.M. / Borges, R.J. / Fontes, M.R.M.
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2021
Title: The synthetic varespladib molecule is a multi-functional inhibitor for PLA 2 and PLA 2 -like ophidic toxins.
Authors: Salvador, G.H.M. / Borges, R.J. / Lomonte, B. / Lewin, M.R. / Fontes, M.R.M.
History
DepositionMar 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Basic phospholipase A2 homolog BomoTx
B: Basic phospholipase A2 homolog BomoTx
C: Basic phospholipase A2 homolog BomoTx
D: Basic phospholipase A2 homolog BomoTx
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2339
Polymers55,3574
Non-polymers1,8765
Water8,053447
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint7 kcal/mol
Surface area24660 Å2
Unit cell
Length a, b, c (Å)60.749, 128.595, 67.790
Angle α, β, γ (deg.)90.000, 106.600, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-331-

HOH

21A-423-

HOH

31B-307-

HOH

41B-324-

HOH

51B-362-

HOH

61B-368-

HOH

71C-306-

HOH

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Components

#1: Protein
Basic phospholipase A2 homolog BomoTx / svPLA2 homolog


Mass: 13839.158 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bothrops moojeni (Brazilian lancehead) / Tissue: Venom Gland / References: UniProt: A0A1S5XW05
#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.: 4 / Source method: obtained synthetically / Formula: C21H20N2O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 46.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 32% w/v PEG4000, 0.1 M Tris HCl, 0.1 M 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: Dec 12, 2018 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.425 Å / Relative weight: 1
ReflectionResolution: 1.758→32.483 Å / Num. obs: 328716 / % possible obs: 99.09 % / Redundancy: 6.7 % / Biso Wilson estimate: 30.4 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.025 / Rrim(I) all: 0.064 / Net I/σ(I): 19.98
Reflection shellResolution: 1.758→1.82 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 1.24 / Num. unique obs: 49048 / CC1/2: 0.584 / CC star: 0.859 / Rpim(I) all: 0.604 / Rrim(I) all: 0.159 / % possible all: 97.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.33 Å47.6 Å
Translation6.33 Å47.6 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.8.1phasing
PHENIX1.13-2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CE2

6ce2


Resolution: 1.758→32.483 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2256 3940 4.08 %
Rwork0.1936 92550 -
obs0.1948 96490 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.4 Å2 / Biso mean: 45.3403 Å2 / Biso min: 20.83 Å2
Refinement stepCycle: final / Resolution: 1.758→32.483 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3735 0 136 447 4318
Biso mean--40.21 45.7 -
Num. residues----488
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.758-1.7790.3771360.3845322494
1.779-1.80150.37991380.3628324298
1.8015-1.82520.34461400.3373336398
1.8252-1.85020.34271400.3289324598
1.8502-1.87670.31561410.2975335098
1.8767-1.90470.32171400.3083324098
1.9047-1.93440.33981420.2841329198
1.9344-1.96610.31161430.2761333999
1.9661-20.29021390.2667330698
2-2.03640.2691410.2701331999
2.0364-2.07560.32171400.259326998
2.0756-2.11790.30881420.2481330099
2.1179-2.1640.31691440.2405334799
2.164-2.21430.25731370.2216328399
2.2143-2.26960.29241430.2219338099
2.2696-2.3310.23491400.2136332599
2.331-2.39960.21461440.20123313100
2.3996-2.4770.23621370.2013360100
2.477-2.56550.22241430.20383342100
2.5655-2.66820.24751420.2065332799
2.6682-2.78950.22861430.1948334099
2.7895-2.93650.20891410.1965328498
2.9365-3.12030.24291430.1959330899
3.1203-3.3610.19281420.1806333199
3.361-3.69880.23281370.161318195
3.6988-4.23310.16541450.144332299
4.2331-5.32940.16241440.14143345100
5.3294-32.4830.18851330.1617327497
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)
19.0861-1.91021.165.2576-1.86442.17870.19540.1920.4992-0.0095-0.1205-0.60640.04110.21620.04250.272-0.03560.01290.3022-0.05230.3474-0.055617.399865.4688
24.3801-1.5640.31533.7538-0.59764.756-0.0141-0.177-0.55210.01280.06410.17230.1762-0.0082-0.08340.17390.0152-0.03740.2188-0.0080.3746-0.78384.338472.6093
36.37250.3731-1.08282.71930.84597.5079-0.16310.8109-0.9317-1.00930.0875-0.35350.01720.2632-0.06980.52570.062-0.1190.4507-0.19870.5271-7.66995.814756.4701
42.2238-1.3197-0.2983.271-0.13631.28530.02030.0626-0.0644-0.13350.00210.276-0.12070.0316-0.08320.2585-0.0042-0.06990.2633-0.04780.3815-7.965315.058268.1492
54.74976.4006-1.18812.0996-1.30233.3687-0.2429-0.08930.3611-0.57340.08070.0277-0.14950.27480.2160.38010.05350.05180.44660.06190.80526.82720.793275.0584
64.80451.15991.5838.55311.65328.6915-0.17030.5616-0.3304-0.0247-0.06340.11740.5320.47120.20580.2781-0.04420.05420.2998-0.04180.2192-0.999535.612864.6471
72.8784-0.60230.9874.32-2.27272.544-0.02370.30080.10690.4999-0.04270.8835-0.22890.05430.02570.2399-0.05840.1060.2735-0.04990.3834-8.743146.039859.4502
86.5752-0.7671-0.04035.1342-1.09055.85860.5353-0.1270.34520.3716-0.5755-0.1596-0.52890.32030.01860.4922-0.1811-0.0130.4019-0.00150.29735.384947.290469.6643
91.9252-0.9571-0.44555.4521-1.70420.92540.4619-0.22180.0391.2616-0.1842-0.0397-0.36740.5291-0.21780.4725-0.14450.03430.4181-0.00320.2433-0.998733.675375.7322
104.2567-0.09931.5873.6879-0.43513.83740.18750.1089-0.14330.6309-0.06630.7956-0.10730.0249-0.0280.4373-0.06710.18790.2284-0.04410.4298-9.150340.174464.7695
113.8114-5.23551.03757.842-1.76870.4471-0.06330.94210.4079-0.7855-0.19430.44560.03730.0590.20290.5821-0.0254-0.12540.6654-0.19810.5356-11.053146.680546.9431
128.4077-5.86031.04237.5032-0.56823.2525-0.2274-0.5366-0.27261.01950.47660.84970.4315-1.0449-0.24620.4023-0.03490.12090.34560.00450.4887-14.210957.214559.1335
131.10390.3658-0.43575.1058-0.16096.686-0.02740.0919-0.1287-0.03880.0727-0.63340.68510.3179-0.11620.503-0.0814-0.06670.40490.00930.405517.611953.381392.6252
143.6411.37571.0086.81330.057.2587-0.00880.10820.40780.39940.52610.3028-0.5393-0.3096-0.43910.5572-0.0698-0.01750.38030.10160.325511.000264.145392.7604
154.14721.3820.1614.5387-1.00733.64140.2222-0.72890.08430.8076-0.4078-0.337-0.09260.3250.14760.8221-0.1214-0.18140.48760.04530.352117.032653.5761106.1495
164.80012.47651.70443.09253.84395.4725-0.161-0.77890.30620.9196-0.7112-0.38340.17010.27140.26791.0716-0.15-0.21570.45960.06170.312213.536652.9777111.3003
172.39871.04250.0782.99360.25946.02620.0302-0.121-0.09120.15320.2556-0.0970.0412-0.7485-0.22520.6156-0.1213-0.07580.35860.08170.304510.465754.746595.4566
186.1678-0.73882.69585.8238-1.26675.803-0.29572.0454-0.6689-0.6537-1.199-0.4714-0.30320.68081.32220.9028-0.12670.11741.1339-0.06670.574218.147462.787578.5747
199.2019-3.3504-5.35996.44843.53893.5978-0.5630.74670.13310.49920.37940.89790.2335-1.2881-0.12480.7279-0.04980.00840.48250.15720.431410.331372.751388.8707
204.02130.3328-0.75731.9265-0.33511.0387-0.90520.9386-0.4807-0.52170.4495-0.1244-0.44150.1550.31471.0089-0.40980.08840.5725-0.10610.357317.053732.486395.8452
211.7729-1.86191.45762.7063-0.35894.4947-0.14150.139-0.165-0.50370.4463-0.1760.22680.2443-0.35380.5501-0.0992-0.00460.3628-0.08210.299816.111922.04104.8329
222.542-1.02321.17862.0782-0.67830.6408-0.03560.6995-0.5669-1.49530.27050.2347-0.20720.5484-0.29091.31-0.31850.01650.6572-0.03710.382513.143628.226888.2675
231.8707-0.9043-0.60892.40341.46964.4268-0.01440.2172-0.0927-0.61470.284-0.0799-0.1696-0.1847-0.14940.7499-0.1667-0.05450.34990.0090.259111.340627.5043101.3295
241.40831.9452-1.83847.97110.04884.0616-0.0626-0.84830.07680.0741-0.0545-0.9786-0.02030.02990.07460.58140.0614-0.2020.4827-0.12740.526519.774816.636111.9051
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 21 )A1 - 21
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 53 )A22 - 53
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 65 )A54 - 65
4X-RAY DIFFRACTION4chain 'A' and (resid 66 through 107 )A66 - 107
5X-RAY DIFFRACTION5chain 'A' and (resid 108 through 122 )A108 - 122
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 13 )B1 - 13
7X-RAY DIFFRACTION7chain 'B' and (resid 14 through 53 )B14 - 53
8X-RAY DIFFRACTION8chain 'B' and (resid 54 through 65 )B54 - 65
9X-RAY DIFFRACTION9chain 'B' and (resid 66 through 79 )B66 - 79
10X-RAY DIFFRACTION10chain 'B' and (resid 80 through 107 )B80 - 107
11X-RAY DIFFRACTION11chain 'B' and (resid 108 through 115 )B108 - 115
12X-RAY DIFFRACTION12chain 'B' and (resid 116 through 122 )B116 - 122
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 31 )C1 - 31
14X-RAY DIFFRACTION14chain 'C' and (resid 32 through 53 )C32 - 53
15X-RAY DIFFRACTION15chain 'C' and (resid 54 through 72 )C54 - 72
16X-RAY DIFFRACTION16chain 'C' and (resid 73 through 79 )C73 - 79
17X-RAY DIFFRACTION17chain 'C' and (resid 80 through 107 )C80 - 107
18X-RAY DIFFRACTION18chain 'C' and (resid 108 through 115 )C108 - 115
19X-RAY DIFFRACTION19chain 'C' and (resid 116 through 122 )C116 - 122
20X-RAY DIFFRACTION20chain 'D' and (resid 1 through 13 )D1 - 13
21X-RAY DIFFRACTION21chain 'D' and (resid 14 through 53 )D14 - 53
22X-RAY DIFFRACTION22chain 'D' and (resid 54 through 79 )D54 - 79
23X-RAY DIFFRACTION23chain 'D' and (resid 80 through 107 )D80 - 107
24X-RAY DIFFRACTION24chain 'D' and (resid 108 through 122 )D108 - 122

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