[English] 日本語
Yorodumi
- PDB-3e8y: Xray structure of scorpion toxin BmBKTx1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3e8y
TitleXray structure of scorpion toxin BmBKTx1
ComponentsPotassium channel toxin alpha-KTx 19.1
KeywordsTOXIN / racemic protein / direct methods / Xray crystal stucture / Ionic channel inhibitor / Neurotoxin / Potassium channel inhibitor / Secreted
Function / homologyScorpion short toxins signature. / Scorpion short chain toxin, potassium channel inhibitor / Scorpion short toxin, BmKK2 / Knottin, scorpion toxin-like superfamily / ion channel inhibitor activity / potassium channel regulator activity / toxin activity / extracellular region / Potassium channel toxin alpha-KTx 19.1
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.1 Å
AuthorsMandal, K. / Pentelute, B.L. / Tereshko, V. / Kossiakoff, A.A. / Kent, S.B.H.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: X-ray structure of native scorpion toxin BmBKTx1 by racemic protein crystallography using direct methods.
Authors: Mandal, K. / Pentelute, B.L. / Tereshko, V. / Kossiakoff, A.A. / Kent, S.B.
History
DepositionAug 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
X: Potassium channel toxin alpha-KTx 19.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,4803
Polymers3,3481
Non-polymers1322
Water36020
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.633, 56.633, 31.759
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number88
Space group name H-MI41/a

-
Components

#1: Protein/peptide Potassium channel toxin alpha-KTx 19.1 / Neurotoxin BmBKTx1 / BmK37


Mass: 3348.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemical synthesis / References: UniProt: P83407
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 1.9 Å3/Da / Density % sol: 35.31 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 0.1 M citric acid, 2 M ammonium sulfate, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97911 Å
DetectorType: MAR CCD 300 / Detector: CCD / Date: Aug 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.1→20 Å / Num. obs: 17925 / % possible obs: 99.78 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 10.1 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 41.6
Reflection shellResolution: 1.1→1.129 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 2.35 / % possible all: 97.33

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.1→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.956 / SU B: 0.453 / SU ML: 0.01 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.03 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21737 2035 10.2 %RANDOM
Rwork0.20006 ---
obs0.20175 17925 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.096 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms240 0 6 22 268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022255
X-RAY DIFFRACTIONr_angle_refined_deg1.921.996348
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.074541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.906245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9661555
X-RAY DIFFRACTIONr_chiral_restr0.1240.237
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02175
X-RAY DIFFRACTIONr_nbd_refined0.2110.291
X-RAY DIFFRACTIONr_nbtor_refined0.3120.2178
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.210
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0950.25
X-RAY DIFFRACTIONr_mcbond_it2.2441.5174
X-RAY DIFFRACTIONr_mcangle_it3.2152270
X-RAY DIFFRACTIONr_scbond_it4.556396
X-RAY DIFFRACTIONr_scangle_it5.3354.572
X-RAY DIFFRACTIONr_rigid_bond_restr2.2973270
X-RAY DIFFRACTIONr_sphericity_free10.207323
X-RAY DIFFRACTIONr_sphericity_bonded5.9283245
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 149 -
Rwork0.27 1275 -
obs--97.33 %

+
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