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- PDB-4yv5: Crystal Structure of Myotoxin II from Bothrops moojeni complexed ... -

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Basic information

Entry
Database: PDB / ID: 4yv5
TitleCrystal Structure of Myotoxin II from Bothrops moojeni complexed to Suramin
ComponentsBasic phospholipase A2 homolog 2
KeywordsTOXIN / Bothrops moojeni / Myotoxin II / Lys49-PLA2 / Suramin
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-SVR / Basic phospholipase A2 homolog myotoxin II
Similarity search - Component
Biological speciesBothrops moojeni (Brazilian lancehead)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsSalvador, G.H.M. / Fontes, M.R.M.
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2015
Title: Structural and functional evidence for membrane docking and disruption sites on phospholipase A2-like proteins revealed by complexation with the inhibitor suramin.
Authors: Salvador, G.H. / Dreyer, T.R. / Cavalcante, W.L. / Matioli, F.F. / Dos Santos, J.I. / Velazquez-Campoy, A. / Gallacci, M. / Fontes, M.R.
History
DepositionMar 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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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)31,92214
Polymers27,8242
Non-polymers4,09812
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-160 kcal/mol
Surface area13080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.795, 63.646, 87.721
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules BA

#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) / References: UniProt: Q9I834

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Non-polymers , 5 types, 209 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 / Polyethylene glycol


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-SVR / 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFON IC ACID / SURAMIN / Suramin


Mass: 1297.280 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C51H40N6O23S6 / Comment: medication*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.55 Å3/Da / Density % sol: 51.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% (w/v) PEG 4000, 0.1 M Tris HCl pH 8.5 and 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: Apr 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.425 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 23072 / % possible obs: 99.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 20.52 Å2 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.066 / Rrim(I) all: 0.144 / Χ2: 0.948 / Net I/av σ(I): 10.814 / Net I/σ(I): 5.9 / Num. measured all: 108433
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.974.90.722630.7110.360.7890.81399.9
1.97-2.054.90.45522720.850.2310.5120.772100
2.05-2.144.90.38322760.8590.1970.4320.919100
2.14-2.254.80.30522770.9030.1590.3451.01399.9
2.25-2.394.70.24422820.9230.1280.2760.998100
2.39-2.584.60.18822830.9620.0990.2140.964100
2.58-2.844.50.16523100.9670.0880.1881.02100
2.84-3.254.30.11923120.9860.0640.1361.012100
3.25-4.094.60.07623350.9930.0390.0850.94599.8
4.09-504.80.05324620.9960.0260.061.03998.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.9 Å31.82 Å
Translation1.9 Å31.82 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
SCALEPACKdata scaling
PHASER2.5.3phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KF3

4kf3


Resolution: 1.9→31.823 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2272 1152 5 %Random
Rwork0.1948 21875 --
obs0.1964 23027 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.82 Å2 / Biso mean: 26.1892 Å2 / Biso min: 8.52 Å2
Refinement stepCycle: final / Resolution: 1.9→31.823 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1916 0 263 197 2376
Biso mean--51.7 29.93 -
Num. residues----244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052235
X-RAY DIFFRACTIONf_angle_d1.1353001
X-RAY DIFFRACTIONf_chiral_restr0.037268
X-RAY DIFFRACTIONf_plane_restr0.004357
X-RAY DIFFRACTIONf_dihedral_angle_d18.067834
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.98650.30491420.241726952837100
1.9865-2.09120.25881400.217626822822100
2.0912-2.22220.23211420.201726962838100
2.2222-2.39370.24361430.198327102853100
2.3937-2.63450.25951430.199327102853100
2.6345-3.01540.21881450.209727462891100
3.0154-3.79810.23711450.18627532898100
3.7981-31.82740.18391520.17452883303599
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)
10.0117-0.01030.04650.13580.00050.0615-0.09820.0314-0.033-0.01560.118-0.0564-0.0648-0.0849-0.00380.09090.00180.01040.1375-0.00040.0921-14.08497.184522.933
20.020.01530.03610.04930.02860.067-0.0914-0.0492-0.21660.03350.1660.22530.1704-0.06470.02660.1086-0.02460.00290.16150.0250.1414-18.3949-3.448319.9882
30.06880.10430.02850.0855-0.02310.07390.0315-0.0188-0.0966-0.16140.0035-0.0284-0.0407-0.003800.16820.02610.01040.16950.02320.1949-10.216-11.309223.6652
40.38440.1519-0.12920.1375-0.09460.0846-0.4380.0047-0.23380.06220.1412-0.39770.0781-0.0535-0.13320.15020.0452-0.0710.09530.05180.1403-5.0084-5.189624.4743
50.0781-0.0060.01550.11550.01860.1176-0.1164-0.4434-0.09080.20940.26760.11270.1658-0.0711-0.02750.35850.0448-0.10250.2680.03550.2213-7.90066.260134.9511
60.05490.0286-0.06530.1159-0.050.041-0.1325-0.12610.02450.17720.0497-0.2289-0.1298-0.093-0.00070.1609-0.0026-0.03720.1479-0.02450.1217-6.317715.049421.9361
70.6218-0.5294-0.25150.761-0.27560.6685-0.0141-0.0895-0.1011-0.06160.0801-0.29790.0057-0.0852-0.02690.1398-0.0061-0.00460.1360.02380.1288-8.52870.3719.4388
80.04230.0504-0.00870.0268-0.02810.0037-0.1730.2184-0.18720.18640.08640.29460.0088-0.27950.00890.30220.00190.01230.23510.06170.2819-19.5608-13.712824.4359
90.1253-0.03940.02430.032-0.02630.059-0.2205-0.22910.33040.15950.0808-0.0259-0.11880.06480.00250.17760.00090.05920.19890.01830.3494-3.3833-15.734827.2866
100.04360.0753-0.03380.07760.04240.1089-0.03590.21410.0031-0.05620.00840.03810.09410.2126-0.0160.1143-0.01380.02020.19040.02080.1284-28.2261-14.156133.1523
110.0157-0.0217-0.01370.0264-0.0280.0748-0.08610.3483-0.0344-0.28650.09360.0639-0.0167-0.19470.00190.1708-0.02080.00910.19570.01640.1358-30.4235-6.967226.3664
120.00870.0171-0.03250.0268-0.00580.0425-0.09790.0990.41590.12170.03560.1944-0.3066-0.005-00.2197-0.0083-0.01240.14170.00440.2433-28.89383.816435.3157
130.0678-0.0181-0.03090.1096-0.02350.13390.04430.01760.01030.452-0.00320.1266-0.0336-0.04070.01190.2349-0.0144-0.0130.1498-0.02010.1774-29.5559-1.746442.1341
140.1823-0.08040.13280.11530.08080.380.0024-0.0016-0.08790.18020.0329-0.0918-0.03380.03130.02620.1689-0.0148-0.03540.15430.01350.1659-25.9685-18.197141.3967
150.30820.1839-0.2370.3636-0.20680.2743-0.1582-0.08590.01580.29810.09650.0527-0.2239-0.14510.04960.1415-0.00540.00660.1379-0.01760.1233-32.7779-10.429640.2934
160.00850.0137-0.00320.0302-0.02860.0117-0.05220.53660.3373-0.12050.24340.1399-0.4831-0.4059-0.00010.19780.014-0.02870.21630.07650.2734-35.74163.41826.4241
170.0428-0.00280.07120.4533-0.21750.28270.17620.14340.05830.48770.1734-0.25580.1202-0.20640.00780.2898-0.03950.00120.199-0.01110.247-26.23367.89334.8821
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 13 )B0
2X-RAY DIFFRACTION2chain 'B' and (resid 15 through 27 )B0
3X-RAY DIFFRACTION3chain 'B' and (resid 28 through 39 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 40 through 57 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 58 through 74 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 75 through 88 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 89 through 117 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 118 through 126 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 127 through 133 )B0
10X-RAY DIFFRACTION10chain 'A' and (resid 1 through 13 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 15 through 22 )A0
12X-RAY DIFFRACTION12chain 'A' and (resid 23 through 39 )A0
13X-RAY DIFFRACTION13chain 'A' and (resid 40 through 57 )A0
14X-RAY DIFFRACTION14chain 'A' and (resid 58 through 88 )A0
15X-RAY DIFFRACTION15chain 'A' and (resid 89 through 112 )A0
16X-RAY DIFFRACTION16chain 'A' and (resid 113 through 117 )A0
17X-RAY DIFFRACTION17chain 'A' and (resid 118 through 133 )A0

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