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- PDB-3hzd: Crystal structure of bothropstoxin-I (BthTX-I), a PLA2 homologue ... -

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Basic information

Entry
Database: PDB / ID: 3hzd
TitleCrystal structure of bothropstoxin-I (BthTX-I), a PLA2 homologue from Bothrops jararacussu venom
ComponentsPhospholipase A2 homolog bothropstoxin-1
KeywordsTOXIN / Bothrops / snake venom / Phospholipase A2 / Lys49-PLA2s / myotoxicity / Antibiotic / Antimicrobial / Disulfide bond / Myotoxin / Secreted
Function / homology
Function and homology information


calcium-dependent phospholipase A2 activity / arachidonate 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: 1.91 Å
AuthorsSilva, M.C.O. / Marchi-Salvador, D.P. / Fernandes, C.A.H. / Soares, A.M. / Fontes, M.R.M.
CitationJournal: J.Struct.Biol. / Year: 2010
Title: Comparison between apo and complexed structures of bothropstoxin-I reveals the role of Lys122 and Ca(2+)-binding loop region for the catalytically inactive Lys49-PLA(2)s.
Authors: Fernandes, C.A. / Marchi-Salvador, D.P. / Salvador, G.M. / Silva, M.C. / Costa, T.R. / Soares, A.M. / Fontes, M.R.
History
DepositionJun 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 30, 2011Group: Database references
Revision 1.3Feb 22, 2012Group: Database references
Revision 1.4Apr 3, 2024Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,5133
Polymers27,5062
Non-polymers71
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-15.6 kcal/mol
Surface area12460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.671, 55.671, 127.836
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
11B-201-

LI

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Components

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


Mass: 13753.136 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: The bothropstoxin-I was isolated from the Bothrops jararacussu venom.
Source: (natural) Bothrops jararacussu (jararacussu) / Tissue: venom / References: UniProt: Q90249
#2: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.08 Å3/Da / Density % sol: 40.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 26% PEG 4000, 0.1M Tris-HCl pH 8.5, 0.2M Lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.425 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 14, 2007
RadiationMonochromator: Si curved crystal asymmetrically-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.425 Å / Relative weight: 1
ReflectionResolution: 1.91→26.64 Å / Num. all: 17151 / Num. obs: 16208 / % possible obs: 92 % / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Model not deposited in the PDB but described in paper by M.T. da Silva-Giotto et al., Proteins (1998), 30, pp. 442 454.

Resolution: 1.91→26.64 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.935 / SU B: 11.725 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25209 858 5 %RANDOM
Rwork0.21534 ---
obs0.21725 16208 92.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.503 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0.03 Å20 Å2
2---0.07 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.91→26.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1906 0 1 174 2081
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221960
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8891.992634
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3985240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.0223.84678
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.90915376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2791510
X-RAY DIFFRACTIONr_chiral_restr0.1130.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021442
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.240.21346
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3260.21372
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2232
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3130.282
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3510.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4521.51239
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.24421922
X-RAY DIFFRACTIONr_scbond_it10.1253841
X-RAY DIFFRACTIONr_scangle_it8.2254.5712
X-RAY DIFFRACTIONr_rigid_bond_restr11.16712080
X-RAY DIFFRACTIONr_sphericity_free9.5165181
X-RAY DIFFRACTIONr_sphericity_bonded5.54151906
LS refinement shellResolution: 1.91→1.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 76 -
Rwork0.266 1118 -
obs--91.92 %

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