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- PDB-4wtb: BthTX-I, a svPLA2s-like toxin, complexed with zinc ions -

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Basic information

Entry
Database: PDB / ID: 4wtb
TitleBthTX-I, a svPLA2s-like toxin, complexed with zinc ions
ComponentsBasic phospholipase A2 homolog bothropstoxin-1
KeywordsTOXIN / svPLA2-like inhibitor / BthTX-I
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
Basic phospholipase A2 homolog bothropstoxin-I
Similarity search - Component
Biological speciesBothrops jararacussu (jararacussu)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsBorges, R.J. / Fontes, M.R.M.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)12/06502-5 Brazil
Sao Paulo Research Foundation (FAPESP)09/12155-3 Brazil
CAPES1592/2011 Brazil
CitationJournal: Biochim. Biophys. Acta / Year: 2017
Title: Functional and structural studies of a Phospholipase A2-like protein complexed to zinc ions: Insights on its myotoxicity and inhibition mechanism.
Authors: Borges, R.J. / Cardoso, F.F. / Fernandes, C.A. / Dreyer, T.R. / de Moraes, D.S. / Floriano, R.S. / Rodrigues-Simioni, L. / Fontes, M.R.
History
DepositionOct 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)27,9339
Polymers27,4742
Non-polymers4597
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-138 kcal/mol
Surface area12460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.580, 56.580, 129.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-327-

HOH

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Components

#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: 13737.113 Da / Num. of mol.: 2 / Fragment: UNP residues 17-137 / Source method: isolated from a natural source / Source: (natural) Bothrops jararacussu (jararacussu) / Organ: venom gland / References: UniProt: Q90249
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.1843.54
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop8.5Reservoir solution: 0.1 M TRIS HCl pH 8.5, 30% PEG4k and 0.1M LiSO4 Drop set up: 0.8 uL of protein (10.1 mg/mL), 0.09 uL of ZnCl2 (1 M), 0.32 uL of MnSO4 (12.5 mM) and 0.48 uL of reservoir solution
2932vapor diffusion, hanging drop8.5Reservoir solution: 0.1 M TRIS HCl pH 8.5, 30% PEG4k and 0.1M LiSO4 Drop set up: 0.8 uL of protein (10.1 mg/mL), 0.09 uL of ZnCl2 (1 M), 0.32 uL of MnSO4 (12.5 mM) and 0.48 uL of reservoir solution

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1801
2802
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONLNLS D03B-MX111.608
SYNCHROTRONLNLS W01B-MX221.283
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDSep 15, 2011
MARMOSAIC 225 mm CCD2CCDJun 22, 2012
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.6081
21.2831
ReflectionResolution: 2.16→45.84 Å / Num. obs: 13020 / % possible obs: 96.5 % / Redundancy: 3.9 % / Net I/σ(I): 13.17
Reflection shellResolution: 2.16→2.28 Å / Mean I/σ(I) obs: 2.02 / % possible all: 99.6

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Processing

SoftwareName: PHENIX / Version: 1.9_1692 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3HZD

3hzd


Resolution: 2.16→45.83 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 25.58 / Stereochemistry target values: ML
Details: Hexagonal crystals data set used to structure refinement. Hexagonal isomorphous crystal data set used to locate zinc.
RfactorNum. reflection% reflectionSelection details
Rfree0.2339 651 5 %Random selection
Rwork0.1905 ---
obs0.1927 13016 96.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.16→45.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1853 0 15 116 1984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041969
X-RAY DIFFRACTIONf_angle_d0.8832640
X-RAY DIFFRACTIONf_dihedral_angle_d12.439726
X-RAY DIFFRACTIONf_chiral_restr0.032272
X-RAY DIFFRACTIONf_plane_restr0.004340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.3280.36471280.27962443X-RAY DIFFRACTION97
2.328-2.56230.23231320.21182493X-RAY DIFFRACTION100
2.5623-2.9330.24551310.19262500X-RAY DIFFRACTION99
2.933-3.69510.20171300.17042458X-RAY DIFFRACTION97
3.6951-45.84040.22691300.17922471X-RAY DIFFRACTION91

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