[English] 日本語
Yorodumi
- PDB-1b7d: NEUROTOXIN (TS1) FROM BRAZILIAN SCORPION TITYUS SERRULATUS -

+
Open data


ID or keywords:

Loading...

-
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
LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / Scorpion long chain toxin / 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 ...LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / Scorpion long chain toxin / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Phosphate


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


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Processing

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more