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- PDB-6dik: Crystal structure of Bothropstoxin I (BthTX-I) complexed to Chico... -

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Basic information

Entry
Database: PDB / ID: 6dik
TitleCrystal structure of Bothropstoxin I (BthTX-I) complexed to Chicoric acid
ComponentsBasic phospholipase A2 homolog bothropstoxin-1
KeywordsTOXIN / Bothropd jararacussu / BthTX-I / Inhibitor / Chicoric Acid / Cichoric Acid / PLA2
Function / homology
Function and homology information


calcium-dependent phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / phospholipid binding / heparin binding / toxin activity / 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
BICARBONATE ION / ETHANOL / Chem-GKP / Basic phospholipase A2 homolog bothropstoxin-I
Similarity search - Component
Biological speciesBothrops jararacussu (jararacussu)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.93 Å
AuthorsCardoso, F.F. / Salvador, G.H.M. / Borges, R.J.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2012/07112-6 Brazil
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2018
Title: Structural basis of phospholipase A2-like myotoxin inhibition by chicoric acid, a novel potent inhibitor of ophidian toxins.
Authors: Cardoso, F.F. / Borges, R.J. / Dreyer, T.R. / Salvador, G.H.M. / Cavalcante, W.L.G. / Pai, M.D. / Gallacci, M. / Fontes, M.R.M.
History
DepositionMay 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Basic phospholipase A2 homolog bothropstoxin-1
B: Basic phospholipase A2 homolog bothropstoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,56610
Polymers27,5042
Non-polymers1,0628
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-74 kcal/mol
Surface area13400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.558, 71.632, 44.791
Angle α, β, γ (deg.)90.000, 109.020, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Basic phospholipase A2 homolog bothropstoxin-1 / svPLA2 homolog / BOJU-I / Bothropstoxin I / BtxtxI / Myotoxic phospholipase A2-like / Phospholipase ...svPLA2 homolog / BOJU-I / Bothropstoxin I / BtxtxI / Myotoxic phospholipase A2-like / Phospholipase A2 homolog 1


Mass: 13752.150 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bothrops jararacussu (jararacussu) / Tissue: Venom glands / References: UniProt: Q90249

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Non-polymers , 5 types, 216 molecules

#2: Chemical ChemComp-GKP / (2R,3R)-2,3-bis{[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}butanedioic acid / Chicoric acid


Mass: 474.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H18O12
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.18 Å3/Da / Density % sol: 43.61 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 30% PEG4000, 0.1M Tris HCl, 0.1M 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: Feb 12, 2014 / Details: Mirrors
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.425 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 17613 / % possible obs: 97.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 28.68 Å2 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.058 / Rrim(I) all: 0.104 / Χ2: 0.945 / Net I/σ(I): 11.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.93-23.20.25717860.9160.1690.310.80699.8
2-2.083.20.20917780.9190.1380.2520.99599.8
2.08-2.173.20.15718000.9530.1040.1890.90499.9
2.17-2.293.20.1517790.9580.0990.181.01899.4
2.29-2.433.20.11717780.9750.0760.140.86499.2
2.43-2.623.20.11517810.9750.0750.1380.97299.1
2.62-2.883.20.10517490.9780.0690.126197.4
2.88-3.33.20.09117420.9830.0610.110.96496.3
3.3-4.1630.07417010.9880.0510.090.93594.3
4.16-502.90.06317190.9890.0450.0780.99792.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IQ3

3iq3


Resolution: 1.93→27.346 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.52
RfactorNum. reflection% reflection
Rfree0.2004 884 5.02 %
Rwork0.1646 --
obs0.1664 17595 97.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.48 Å2 / Biso mean: 34.959 Å2 / Biso min: 15.74 Å2
Refinement stepCycle: final / Resolution: 1.93→27.346 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1869 0 66 208 2143
Biso mean--54.32 39.65 -
Num. residues----242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041997
X-RAY DIFFRACTIONf_angle_d0.6942695
X-RAY DIFFRACTIONf_chiral_restr0.044267
X-RAY DIFFRACTIONf_plane_restr0.004342
X-RAY DIFFRACTIONf_dihedral_angle_d16.1691234
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9204-2.04070.23471480.18822733288196
2.0407-2.19820.21661490.166228553004100
2.1982-2.41930.23021500.16682827297799
2.4193-2.7690.26831490.17972813296299
2.769-3.48760.19151480.16982760290896
3.4876-27.3490.16411400.15062723286394
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)
18.12591.9519-1.94215.5649-1.08774.71590.13050.3426-0.4901-0.1782-0.0188-0.01280.2772-0.0914-0.11310.26610.0582-0.01770.2180.00020.19023.6808-10.5149.8614
21.6471.06681.19133.04134.42056.6298-0.14610.1255-0.028-0.310.3881-0.1814-0.3930.198-0.20620.23030.01370.0020.21790.03920.2038-0.73310.90317.887
39.10923.3262-6.04787.71550.09586.24820.3029-0.85120.09790.4738-0.0776-0.0462-0.27590.6356-0.07930.3430.0352-0.03170.3318-0.00540.22661.663310.033816.0972
48.46782.448-2.64223.54650.52752.62850.0297-0.3952-0.06020.00980.1886-0.2566-0.35530.2958-0.14290.2535-0.0002-0.03540.2404-0.02690.23726.54982.466517.6165
53.5058-0.9555-1.50936.1904-0.75044.56690.0471-0.1393-0.2287-0.4733-0.2824-0.91590.02321.01580.04440.24510.05480.03610.38210.0370.402216.7187-8.243711.0378
63.2453.12671.11953.20480.50991.9580.2615-0.1724-0.64610.3411-0.1798-0.29280.27040.2699-0.04290.30580.07390.0290.22290.02190.35537.0982-17.60417.6617
76.802-3.21170.03822.9863-0.36871.8492-0.1609-0.2399-0.03770.16590.1247-0.07230.0376-0.00870.07640.20960.0089-0.01370.1581-0.01340.17971.7555-4.016216.5192
85.1025-0.41271.81350.07650.06763.8229-0.27990.04020.6574-0.18320.26150.025-0.97570.29880.17470.4970.02640.02280.30690.0430.3614-1.703211.89926.1007
93.42813.5078-0.71488.4864.31885.8061-0.0467-0.6608-0.184-0.04310.4507-0.6481-0.84130.0212-0.49870.3286-0.0418-0.030.2669-0.00790.46036.967213.732518.623
106.4732-1.4762.17496.72720.93852.23790.2037-0.54180.40140.75550.0290.3719-0.4311-0.015-0.20310.3089-0.0510.05820.2769-0.03280.23628.372513.4274-5.8802
114.3659-0.1918-1.12725.3031-1.01543.2871-0.0518-0.37140.0510.45220.2384-0.0040.1621-0.3083-0.17580.2669-0.07370.03290.2747-0.0180.16881.22253.9948-5.7075
123.012-2.9756-0.35743.0981.01823.4796-0.1913-0.7279-0.59940.3080.1921-0.32020.4368-0.0088-0.01960.3675-0.02480.01130.31630.03440.368.6266-5.4991-7.0099
132.5904-2.01943.48723.5091-1.47435.95420.02780.48180.36230.0058-0.0611-0.40580.39050.61560.02180.25010.01780.01480.25750.01330.283813.6855-0.5003-9.9137
141.65682.0317-1.31643.6826-0.67536.07350.6877-1.0592-0.02471.1192-0.4666-0.8109-0.36751.2007-0.32810.5165-0.2551-0.12870.59860.05040.385320.55210.3209-0.5705
158.2581-0.40490.9273.182-0.31453.30760.0261-0.10080.19030.189-0.2837-0.6436-0.24750.14750.27130.2828-0.06350.01880.21920.03380.353215.545419.6973-11.5665
167.61233.0011.86873.60270.83713.2081-0.0344-0.0376-0.04450.2086-0.0906-0.3157-0.26270.35350.11110.2417-0.0385-0.00570.24110.0420.253715.52859.652-11.3371
178.55135.105-2.58383.4666-3.14016.7872-0.2960.1524-0.28040.19570.3290.19350.7277-1.06140.00240.2956-0.07840.02650.3069-0.06170.2382-2.153-0.6228-12.9751
184.2695-5.17170.17636.2883-0.03763.6195-0.5958-0.3636-0.49950.69920.69380.35550.5025-0.20980.0210.401-0.04750.06150.33610.00910.33090.5526-7.9603-2.6519
192.7328-4.29111.01529.40820.55712.1118-0.27930.7270.7754-0.15820.5027-0.47190.80680.0902-0.27870.4954-0.00080.12420.3762-0.01020.548514.0766-11.7214-9.3257
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 32 )A15 - 32
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 39 )A33 - 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 90 through 117 )A90 - 117
8X-RAY DIFFRACTION8chain 'A' and (resid 118 through 125 )A118 - 125
9X-RAY DIFFRACTION9chain 'A' and (resid 126 through 133 )A126 - 133
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 13 )B1 - 13
11X-RAY DIFFRACTION11chain 'B' and (resid 15 through 27 )B15 - 27
12X-RAY DIFFRACTION12chain 'B' and (resid 28 through 39 )B28 - 39
13X-RAY DIFFRACTION13chain 'B' and (resid 40 through 57 )B40 - 57
14X-RAY DIFFRACTION14chain 'B' and (resid 58 through 74 )B58 - 74
15X-RAY DIFFRACTION15chain 'B' and (resid 75 through 88 )B75 - 88
16X-RAY DIFFRACTION16chain 'B' and (resid 90 through 108 )B90 - 108
17X-RAY DIFFRACTION17chain 'B' and (resid 109 through 117 )B109 - 117
18X-RAY DIFFRACTION18chain 'B' and (resid 118 through 125 )B118 - 125
19X-RAY DIFFRACTION19chain 'B' and (resid 126 through 133 )B126 - 133

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