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- PDB-1b7d: NEUROTOXIN (TS1) FROM BRAZILIAN SCORPION TITYUS SERRULATUS -

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Basic information

Entry
Database: PDB / ID: 1b7d
TitleNEUROTOXIN (TS1) FROM BRAZILIAN SCORPION TITYUS SERRULATUS
ComponentsPROTEIN (NEUROTOXIN TS1)
KeywordsTOXIN / LONG-CHAIN 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: 1.73 Å
AuthorsPolikarpov, I. / Sanches Jr., M.S. / Marangoni, S. / Toyama, M.H. / Teplyakov, A.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of neurotoxin Ts1 from Tityus serrulatus provides insights into the specificity and toxicity of scorpion toxins.
Authors: Polikarpov, I. / Junior, M.S. / Marangoni, S. / Toyama, M.H. / Teplyakov, A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallisation and Preliminary Diffraction Data of Neurotoxin Ts-Gamma from the Venom of Scorpion Tityus Serrulatus
Authors: Golubev, A.M. / Lee, W.H. / Marangoni, S. / Novello, J.C. / Oliveira, B. / Toyama, M.H.
History
DepositionJan 21, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 22, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (NEUROTOXIN TS1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9962
Polymers6,9011
Non-polymers951
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)22.210, 36.540, 31.720
Angle α, β, γ (deg.)90.00, 100.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN (NEUROTOXIN TS1)


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


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 1.81 Å3/Da / Density % sol: 32.84 %
Description: DIFFRACTION DATA HAVE BEEN COLLECTED AT THE LABORATORIO NACIONAL DE LUZ SINCROTRON (LNLS), CAMPINAS, BRAZIL
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: 0.01ml protein solution was mixed with 0.005ml reservoir
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: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.37
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: CYLINDRICAL MIRROR
RadiationMonochromator: SI BENT SINGLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.37 Å / Relative weight: 1
ReflectionResolution: 1.73→13 Å / Num. obs: 5149 / % possible obs: 97.1 % / Redundancy: 2.6 % / Rsym value: 0.066
Reflection shellResolution: 1.73→1.77 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 3 / Rsym value: 0.26 / % possible all: 81.6
Reflection
*PLUS
Num. measured all: 13402 / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 81.6 % / Rmerge(I) obs: 0.26

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AHO

1aho


Resolution: 1.73→13 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.238 -5 %RANDOM
Rwork0.178 ---
obs-5149 97.1 %-
Displacement parametersBiso mean: 21.1 Å2
Refinement stepCycle: LAST / Resolution: 1.73→13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms483 0 5 65 553
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0320.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0320.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.4043
X-RAY DIFFRACTIONp_mcangle_it3.385
X-RAY DIFFRACTIONp_scbond_it4.6986
X-RAY DIFFRACTIONp_scangle_it6.4818
X-RAY DIFFRACTIONp_plane_restr0.0270.04
X-RAY DIFFRACTIONp_chiral_restr0.1440.15
X-RAY DIFFRACTIONp_singtor_nbd0.1770.3
X-RAY DIFFRACTIONp_multtor_nbd0.270.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1810.3
X-RAY DIFFRACTIONp_planar_tor4.37
X-RAY DIFFRACTIONp_staggered_tor12.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor1020
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.7

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