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- PDB-6mqd: Myotoxin II from Bothrops moojeni complexed with Rosmarinic Acid -

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Basic information

Entry
Database: PDB / ID: 6mqd
TitleMyotoxin II from Bothrops moojeni complexed with Rosmarinic Acid
ComponentsBasic phospholipase A2 homolog 2
KeywordsTOXIN / Rosmarinic Acid / Snake Venom
Function / homology
Function and homology information


calcium-dependent phospholipase A2 activity / arachidonate secretion / defense response to fungus / negative regulation of T cell proliferation / lipid catabolic process / phospholipid metabolic process / 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 / negative regulation of T cell proliferation / lipid catabolic process / phospholipid metabolic process / 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-ROA / Basic phospholipase A2 homolog myotoxin II
Similarity search - Component
Biological speciesBothrops moojeni (Brazilian lancehead)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)28,1853
Polymers27,8242
Non-polymers3601
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-18 kcal/mol
Surface area13050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.076, 65.839, 90.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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-ROA / (2R)-3-(3,4-dihydroxyphenyl)-2-{[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}propanoic acid / Rosmarinic acid


Mass: 360.315 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H16O8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H2O
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: 2.46 Å3/Da / Density % sol: 50.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 4000, Tris HCl, 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: 1.459 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 37066 / % possible obs: 99.7 % / Redundancy: 9.7 % / Biso Wilson estimate: 15.67 Å2 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.033 / Rrim(I) all: 0.111 / Χ2: 1.006 / Net I/σ(I): 8.8 / Num. measured all: 359908
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.674.70.72344790.7350.3740.8180.98798.3
1.67-1.766.50.55845580.8830.2380.6080.98699.9
1.76-1.8780.37845970.950.1430.4051.07199.9
1.87-2.029.10.24546120.980.0860.261.023100
2.02-2.2211.50.16146060.9930.0490.1680.984100
2.22-2.5412.50.12946430.9960.0380.1340.975100
2.54-3.212.70.09346760.9980.0270.0971.026100
3.2-5012.30.06848950.9980.020.0711.00499.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.6 Å23.55 Å
Translation1.6 Å23.55 Å

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Processing

Software
NameVersionClassification
HKL-20001.8.4data scaling
PHASER2.5.6phasing
PHENIX1.12refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6B80

6b80


Resolution: 1.6→23.554 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.91
RfactorNum. reflection% reflection
Rfree0.191 1851 5 %
Rwork0.1571 --
obs0.1589 37010 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 75.96 Å2 / Biso mean: 21.1806 Å2 / Biso min: 9.02 Å2
Refinement stepCycle: final / Resolution: 1.6→23.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1913 0 25 392 2330
Biso mean--34.98 31.85 -
Num. residues----244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131992
X-RAY DIFFRACTIONf_angle_d1.5742654
X-RAY DIFFRACTIONf_chiral_restr0.063269
X-RAY DIFFRACTIONf_plane_restr0.009341
X-RAY DIFFRACTIONf_dihedral_angle_d11.805755
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5991-1.64230.23661400.20552660280099
1.6423-1.69060.23881360.19882585272198
1.6906-1.74520.22731410.169226812822100
1.7452-1.80750.22211400.163426652805100
1.8075-1.87990.19561420.156326842826100
1.8799-1.96540.20691410.163526852826100
1.9654-2.06890.20871410.156326952836100
2.0689-2.19850.19311430.142527062849100
2.1985-2.36810.18231420.151526952837100
2.3681-2.60610.181420.15127002842100
2.6061-2.98260.19171440.161727382882100
2.9826-3.75530.17081460.146427722918100
3.7553-23.55620.18191530.158128933046100
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)
13.665-1.31193.10864.6618-0.52918.7013-0.05350.14410.1278-0.0341-0.0415-0.1836-0.23810.29970.12250.0927-0.01330.00340.10070.01380.145110.4872-9.6689-17.7184
24.9752-1.7121-4.63777.15574.54926.1193-0.0534-0.02830.27420.08760.1539-0.3607-0.14690.3779-0.06210.1075-0.02350.00070.1282-0.00610.117718.4284-15.4575-15.9422
32.99362.3013-0.62695.35210.18943.2765-0.0560.0884-0.1295-0.21570.12870.00070.0457-0.0145-0.0580.09190.00680.00560.0958-0.00750.11413.3275-26.933-21.688
47.6487-2.41693.81843.2783-0.29723.08460.00220.0362-0.1198-0.1388-0.02040.2166-0.086-0.1492-0.02830.1134-0.02550.01410.0849-0.00630.10745.2204-23.5009-21.2304
54.82940.29660.89976.03172.29587.60650.05780.35850.0414-0.52820.05080.00470.03690.2189-0.0660.18080.0124-0.02850.11790.02430.09132.7843-10.0529-28.7239
63.5255-0.1254-0.30014.738-0.50943.1502-0.0964-0.70730.19880.35750.070.0088-0.3107-0.18030.03220.16020.0177-0.00530.1529-0.03350.12650.4071-4.9765-14.4059
74.3841-3.88683.39155.1635-3.67324.2397-0.0425-0.1349-0.15760.14030.12280.2393-0.1335-0.1119-0.09590.111-0.01560.00760.0918-0.00050.12424.0704-16.0419-15.7207
87.6931-5.1802-2.42446.8944-0.31222.78890.0865-0.4166-0.31480.1548-0.0547-0.44830.29180.68240.00170.12570.0012-0.02220.19370.04710.203220.5639-26.0839-13.3418
97.49442.48420.34852.5825-0.36591.7026-0.15070.0413-0.2158-0.16820.0067-0.00850.01990.0560.13650.17-0.00290.030.1207-0.02230.160615.1879-30.2393-24.5966
101.9496-0.9013-0.11853.90151.29652.64330.0327-0.0484-0.0590.0697-0.00280.02550.1334-0.0144-0.03530.0994-0.00850.00130.11060.02210.087227.9996-30.2418-33.8678
119.34020.05962.18087.7836-2.11494.409-0.08110.26580.6762-0.2356-0.00670.1526-0.2241-0.060.12720.21360.0162-0.00190.15960.00010.145325.0574-15.0959-37.4893
127.7080.49163.98473.75891.26416.4051-0.06230.18030.1273-0.3182-0.00430.2588-0.2908-0.1055-0.01120.15890.0138-0.01530.10190.02050.107624.3743-22.4107-42.0802
138.9166-1.1241-0.8834.4971.26913.7084-0.03530.0191-0.26830.0062-0.01650.08520.10150.00920.07660.1733-0.0217-0.01930.142-0.03370.108324.2747-37.7153-44.4083
146.57695.14844.52316.04094.11044.0507-0.1190.3445-0.1011-0.21750.1110.0294-0.03280.08430.00620.14080.00350.00410.1297-0.00550.094425.9533-33.9952-46.5105
156.7868-2.0672-4.18732.10861.89745.35040.1013-0.29830.12010.0441-0.0144-0.0906-0.2250.2341-0.06530.1488-0.0248-0.00780.0989-0.00220.102129.7094-18.531-29.2494
163.28792.96353.19725.38744.56954.4665-0.4578-0.07750.1347-0.57590.09590.3263-0.4574-0.0030.41240.40070.0754-0.05890.19890.0290.214819.2212-12.8891-41.7653
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 13 )A1 - 13
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 22 )A15 - 22
3X-RAY DIFFRACTION3chain 'A' and (resid 23 through 39 )A23 - 39
4X-RAY DIFFRACTION4chain 'A' and (resid 40 through 57 )A40 - 57
5X-RAY DIFFRACTION5chain 'A' and (resid 58 through 74 )A58 - 74
6X-RAY DIFFRACTION6chain 'A' and (resid 75 through 88 )A75 - 88
7X-RAY DIFFRACTION7chain 'A' and (resid 89 through 112 )A89 - 112
8X-RAY DIFFRACTION8chain 'A' and (resid 113 through 117 )A113 - 117
9X-RAY DIFFRACTION9chain 'A' and (resid 118 through 133 )A118 - 133
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 32 )B1 - 32
11X-RAY DIFFRACTION11chain 'B' and (resid 33 through 39 )B33 - 39
12X-RAY DIFFRACTION12chain 'B' and (resid 40 through 53 )B40 - 53
13X-RAY DIFFRACTION13chain 'B' and (resid 57 through 83 )B57 - 83
14X-RAY DIFFRACTION14chain 'B' and (resid 84 through 108 )B84 - 108
15X-RAY DIFFRACTION15chain 'B' and (resid 109 through 126 )B109 - 126
16X-RAY DIFFRACTION16chain 'B' and (resid 127 through 133 )B127 - 133

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