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- PDB-7rji: BthTX-II variant b, from Bothrops jararacussu venom, complexed wi... -

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Basic information

Entry
Database: PDB / ID: 7rji
TitleBthTX-II variant b, from Bothrops jararacussu venom, complexed with stearic acid
ComponentsBthTX-IIb
KeywordsTOXIN / Basic phospholipase A2 / BthTX-II variant b / Bothrops jararacussu
Function / homologySTEARIC ACID
Function and homology information
Biological speciesBothrops jararacussu (jararacussu)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsBorges, R.J. / Fontes, M.R.M.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)16/24191-8 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)302883/2017-7 Brazil
CitationJournal: Int.J.Biol.Macromol. / Year: 2021
Title: BthTX-II from Bothrops jararacussu venom has variants with different oligomeric assemblies: An example of snake venom phospholipases A 2 versatility.
Authors: Borges, R.J. / Salvador, G.H.M. / Campanelli, H.B. / Pimenta, D.C. / de Oliveira Neto, M. / Uson, I. / Fontes, M.R.M.
History
DepositionJul 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BthTX-IIb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2845
Polymers13,7841
Non-polymers5004
Water77543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.036, 83.036, 124.830
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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Components

#1: Protein BthTX-IIb


Mass: 13783.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Sequence determined using SEQUENCE SLIDER, a methodology that integrates mass spectrometry, crystallographic and genetic data.
Source: (natural) Bothrops jararacussu (jararacussu) / Organ: Venom Gland / References: phospholipase A2
#2: Chemical ChemComp-STE / STEARIC ACID / Stearic acid


Mass: 284.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.02 Å3/Da / Density % sol: 59.27 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 22% polyacrylic acid 5100 (w/v), 20 mM MgCl2, 0.8 mg/mL a-Tocopherol phosphate disodium salt

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45859 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45859 Å / Relative weight: 1
ReflectionResolution: 1.71→40 Å / Num. obs: 34802 / % possible obs: 99.8 % / Redundancy: 17.7 % / Biso Wilson estimate: 31.11 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.1 / Net I/σ(I): 17.26
Reflection shellResolution: 1.71→1.81 Å / Redundancy: 13.5 % / Mean I/σ(I) obs: 1.16 / Num. unique obs: 5598 / CC1/2: 0.564 / Rrim(I) all: 2.382 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Coot1.18.2_3874model building
XDS20210323data reduction
XDS20210323data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2oqd

2oqd


Resolution: 1.71→28.63 Å / SU ML: 0.2138 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.1229
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.224 909 5 %
Rwork0.1977 17285 -
obs0.199 18194 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.75 Å2
Refinement stepCycle: LAST / Resolution: 1.71→28.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms946 0 31 43 1020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00751008
X-RAY DIFFRACTIONf_angle_d1.09961355
X-RAY DIFFRACTIONf_chiral_restr0.0573131
X-RAY DIFFRACTIONf_plane_restr0.006173
X-RAY DIFFRACTIONf_dihedral_angle_d7.2489155
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.810.30321650.27182809X-RAY DIFFRACTION99.3
1.82-1.960.2611450.23572843X-RAY DIFFRACTION99.93
1.96-2.150.25121530.19592850X-RAY DIFFRACTION100
2.15-2.460.23531560.20162868X-RAY DIFFRACTION100
2.46-3.10.24171410.20132912X-RAY DIFFRACTION100
3.1-28.630.19831490.18673003X-RAY DIFFRACTION99.9

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