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- PDB-7rjz: BthTX-II variant a, from Bothrops jararacussu venom, complexed wi... -

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Basic information

Entry
Database: PDB / ID: 7rjz
TitleBthTX-II variant a, from Bothrops jararacussu venom, complexed with benzoic acid
ComponentsBthTX-IIa
KeywordsTOXIN / Basic phospholipase A2 / BthTX-II variant a / Bothrops jararacussu
Function / homologyBENZOIC ACID
Function and homology information
Biological speciesBothrops jararacussu (jararacussu)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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-IIa
B: BthTX-IIa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7204
Polymers27,4762
Non-polymers2442
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-14 kcal/mol
Surface area12810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.400, 107.370, 44.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-345-

HOH

21A-351-

HOH

31A-425-

HOH

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Components

#1: Protein BthTX-IIa


Mass: 13737.836 Da / Num. of mol.: 2 / 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) / References: phospholipase A2
#2: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C7H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.61 Å3/Da / Density % sol: 52.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 0.1 M sodium citrate pH 5.2, 25% PEG4000 (w/v), 0.21 M ammonium sulphate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.0781 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 1.7→40.13 Å / Num. obs: 57103 / % possible obs: 92.9 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rrim(I) all: 0.091 / Net I/σ(I): 11.9
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.15 % / Num. unique obs: 6582 / CC1/2: 0.503 / Rrim(I) all: 1.205 / % possible all: 66.7

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDS20210323data reduction
Coot0.9.5model building
PHASER2.8.3phasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2oqd

2oqd


Resolution: 1.7→40 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2222 1516 5 %Random selection
Rwork0.1891 ---
obs0.1907 30316 93.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1904 0 18 311 2233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031972
X-RAY DIFFRACTIONf_angle_d0.652665
X-RAY DIFFRACTIONf_dihedral_angle_d30.094278
X-RAY DIFFRACTIONf_chiral_restr0.043268
X-RAY DIFFRACTIONf_plane_restr0.005347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.3503890.30251683X-RAY DIFFRACTION61
1.75-1.820.3421140.2762170X-RAY DIFFRACTION78
1.82-1.890.29421390.26232643X-RAY DIFFRACTION96
1.89-1.970.34981430.28162707X-RAY DIFFRACTION97
1.97-2.080.24291430.21822729X-RAY DIFFRACTION98
2.08-2.210.25591440.20132719X-RAY DIFFRACTION98
2.21-2.380.26531440.20212738X-RAY DIFFRACTION98
2.38-2.620.19741470.18052794X-RAY DIFFRACTION99
2.62-30.21551470.18272797X-RAY DIFFRACTION99
3-3.780.1871490.16092838X-RAY DIFFRACTION99
3.78-40.130.18651570.16262982X-RAY DIFFRACTION99

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