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- PDB-5o0u: Crystal structure of tarantula venom peptide Protoxin-II -

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Basic information

Entry
Database: PDB / ID: 5o0u
TitleCrystal structure of tarantula venom peptide Protoxin-II
ComponentsBeta/omega-theraphotoxin-Tp2a
KeywordsTOXIN / Inhibitor cystine knot / ion channel inhibitors / venom
Function / homologysodium channel regulator activity / calcium channel regulator activity / toxin activity / lipid binding / extracellular region / Beta/omega-theraphotoxin-Tp2a
Function and homology information
Biological speciesThrixopelma pruriens (green velvet)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 0.99 Å
AuthorsTabor, A. / McCarthy, S. / Reyes, F.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust109073/Z/15/Z United Kingdom
CitationJournal: J.Am.Chem.Soc. / Year: 2017
Title: The Role of Disulfide Bond Replacements in Analogues of the Tarantula Toxin ProTx-II and Their Effects on Inhibition of the Voltage-Gated Sodium Ion Channel Nav1.7.
Authors: Wright, Z.V.F. / McCarthy, S. / Dickman, R. / Reyes, F.E. / Sanchez-Martinez, S. / Cryar, A. / Kilford, I. / Hall, A. / Takle, A.K. / Topf, M. / Gonen, T. / Thalassinos, K. / Tabor, A.B.
History
DepositionMay 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta/omega-theraphotoxin-Tp2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0355
Polymers3,8401
Non-polymers1954
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint-14 kcal/mol
Surface area3160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.669, 37.669, 103.944
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-1229-

HOH

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Components

#1: Protein/peptide Beta/omega-theraphotoxin-Tp2a / Beta/omega-TRTX-Tp2a / ProTx-II / PT-II / Protoxin-2 / ProTx2


Mass: 3839.687 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thrixopelma pruriens (green velvet) / References: UniProt: P83476
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.85 Å3/Da / Density % sol: 33.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2M lithium sulfate, 100 mM Tris-HCl (pH 8), 2% v/v PEG 400

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 0.99→34.67 Å / Num. obs: 14967 / % possible obs: 92.9 % / Redundancy: 8.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.02 / Net I/σ(I): 25
Reflection shellResolution: 0.993→1.01 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.496 / Num. unique obs: 341 / CC1/2: 0.7 / Rpim(I) all: 0.361 / % possible all: 43.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
SHELXL2016/6refinement
SHARP2.8.5phasing
RefinementMethod to determine structure: SIRAS / Resolution: 0.99→34.65 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.528 / SU ML: 0.012 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.022 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13985 732 4.9 %RANDOM
Rwork0.12601 ---
obs0.12668 14235 92.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.675 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.06 Å2
Refinement stepCycle: 1 / Resolution: 0.99→34.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms258 0 10 54 322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02283
X-RAY DIFFRACTIONr_bond_other_d0.0030.02249
X-RAY DIFFRACTIONr_angle_refined_deg2.1891.906378
X-RAY DIFFRACTIONr_angle_other_deg3.5053576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.192529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.91321.66712
X-RAY DIFFRACTIONr_dihedral_angle_3_deg111553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.561152
X-RAY DIFFRACTIONr_chiral_restr0.1090.233
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02289
X-RAY DIFFRACTIONr_gen_planes_other0.0030.0269
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2380.759119
X-RAY DIFFRACTIONr_mcbond_other1.2420.759118
X-RAY DIFFRACTIONr_mcangle_it1.4711.151147
X-RAY DIFFRACTIONr_mcangle_other1.4671.15148
X-RAY DIFFRACTIONr_scbond_it2.2941.128163
X-RAY DIFFRACTIONr_scbond_other2.2891.135164
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7561.557232
X-RAY DIFFRACTIONr_long_range_B_refined3.7510.817348
X-RAY DIFFRACTIONr_long_range_B_other3.73410.626347
X-RAY DIFFRACTIONr_rigid_bond_restr2.9043528
X-RAY DIFFRACTIONr_sphericity_free44.705537
X-RAY DIFFRACTIONr_sphericity_bonded12.615541
LS refinement shellResolution: 0.993→1.019 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 23 -
Rwork0.229 567 -
obs--50 %

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