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- PDB-1npi: Tityus Serrulatus Neurotoxin (Ts1) at atomic resolution -

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Basic information

Entry
Database: PDB / ID: 1npi
TitleTityus Serrulatus Neurotoxin (Ts1) at atomic resolution
ComponentsToxin VII
KeywordsTOXIN / XCITATORY NEUROTOXIN
Function / homology
Function and homology information


sodium channel inhibitor activity / defense response to fungus / toxin activity / killing of cells of another organism / extracellular region
Similarity search - Function
Scorpion long chain toxin / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / Scorpion long chain toxin/defensin / Scorpion toxin-like domain / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like ...Scorpion long chain toxin / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / Scorpion long chain toxin/defensin / Scorpion toxin-like domain / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Beta-mammal/insect toxin Ts1
Similarity search - Component
Biological speciesTityus serrulatus (Brazilian scorpion)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsPinheiro, C.B. / Marangoni, S. / Toyama, M.H. / Polikarpov, I.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structural analysis of Tityus serrulatus Ts1 neurotoxin at atomic resolution: insights into interactions with Na+ channels.
Authors: Pinheiro, C.B. / Marangoni, S. / Toyama, M.H. / Polikarpov, I.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallization and preliminary diffraction data of neurotoxin Ts-c from the venom of the scorpion Tityus serrulatus
Authors: Golubev, A.M. / Lee, W.H. / Marangoni, S. / Novello, J.C. / Oliveira, B. / Toyama, M.H. / Polikarpov, I.
History
DepositionJan 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Version format compliance
Revision 1.3Aug 16, 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 / 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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Toxin VII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0913
Polymers6,9011
Non-polymers1902
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)23.250, 36.610, 31.100
Angle α, β, γ (deg.)90.00, 105.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Toxin VII / TsTX-VII


Mass: 6901.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tityus serrulatus (Brazilian scorpion) / References: UniProt: P15226
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 1.54 Å3/Da / Density % sol: 13.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 6000, potassium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Details: Golubev, A.M., (1998) Acta Crystallogr., Sect.D, 54, 1440.
PH range low: 6.5 / PH range high: 5.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
215 %(w/v)PEG60001reservoir
350 mMpotassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.28, 1.38
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.281
21.381
ReflectionResolution: 1.16→12.5 Å / Num. all: 16095 / Num. obs: 11943 / % possible obs: 92 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 3 % / Rsym value: 0.078 / Net I/σ(I): 12
Reflection shellResolution: 1.16→1.19 Å / % possible all: 52
Reflection
*PLUS
Lowest resolution: 12 Å / % possible obs: 92 % / Num. measured all: 16095 / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
% possible obs: 52 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata reduction
SHELXmodel building
SHELXL-97refinement
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B7D

1b7d


Resolution: 1.16→12.5 Å / Num. parameters: 5797 / Num. restraintsaints: 5711 / Cross valid method: FREE R / σ(F): 4 / σ(I): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.1391 623 4.9 %RANDOM
Rwork0.0821 ---
all0.1033 16095 --
obs0.0878 12566 78 %-
Refine analyzeNum. disordered residues: 7 / Occupancy sum hydrogen: 442.78 / Occupancy sum non hydrogen: 574.5
Refinement stepCycle: LAST / Resolution: 1.16→12.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms478 0 10 114 602
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0
X-RAY DIFFRACTIONs_angle_d0
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0301
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.056
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.059
X-RAY DIFFRACTIONs_approx_iso_adps0.093
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.1587 / Rfactor Rwork: 0.0974
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONs_bond_d
X-RAY DIFFRACTIONs_angle_d

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