[English] 日本語
Yorodumi
- PDB-1dq7: THREE-DIMENSIONAL STRUCTURE OF A NEUROTOXIN FROM RED SCORPION (BU... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1dq7
TitleTHREE-DIMENSIONAL STRUCTURE OF A NEUROTOXIN FROM RED SCORPION (BUTHUS TAMULUS) AT 2.2A RESOLUTION.
ComponentsNEUROTOXIN
KeywordsTOXIN / Red scorpion Neurotoxin
Function / homology
Function and homology information


sodium channel inhibitor activity / defense response / toxin activity / 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
Biological speciesMesobuthus tamulus (Indian red scorpion)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsSharma, M. / Yadav, S. / Karthikeyan, S. / Kumar, S. / Paramasivam, M. / Srinivasan, A. / Singh, T.P.
CitationJournal: To be Published
Title: Three-dimensional Structure of a Neurotoxin from Red Scorpion (Buthus tamulus) at 2.2A Resolution
Authors: Sharma, M. / Yadav, S. / Karthikeyan, S. / Kumar, S. / Paramasivam, M. / Srinivasan, A. / Singh, T.P.
History
DepositionDec 30, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NEUROTOXIN
B: NEUROTOXIN


Theoretical massNumber of molelcules
Total (without water)14,0942
Polymers14,0942
Non-polymers00
Water1,63991
1
A: NEUROTOXIN


Theoretical massNumber of molelcules
Total (without water)7,0471
Polymers7,0471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NEUROTOXIN


Theoretical massNumber of molelcules
Total (without water)7,0471
Polymers7,0471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.871, 21.001, 52.451
Angle α, β, γ (deg.)90.00, 94.45, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein NEUROTOXIN /


Mass: 7046.870 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mesobuthus tamulus (Indian red scorpion) / Secretion: VENOM / References: UniProt: P60277*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

-
Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.9 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.2
Details: Protein Concentration 7.5mg/ml, Buffer Tris-Hcl 25mM, Percipitant 82% MPD, Additive 0.001 Cacl2, pH 7.2, VAPOR DIFFUSION, SITTING DROP

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 8, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. all: 71526 / Num. obs: 5166 / % possible obs: 87.7 % / Observed criterion σ(I): -3 / Redundancy: 12.5 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 8.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.186 / Num. unique all: 341 / % possible all: 59.3

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementResolution: 2.2→14.92 Å / Rfactor Rfree error: 0.018 / Data cutoff high absF: 453964.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.276 286 5.5 %RANDOM
Rwork0.201 ---
all0.212 71526 --
obs0.201 5176 87.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 115.1 Å2 / ksol: 0.407 e/Å3
Displacement parametersBiso mean: 31.8 Å2
Baniso -1Baniso -2Baniso -3
1--5.27 Å20 Å2-3.16 Å2
2--7.05 Å20 Å2
3----1.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.2→14.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms980 0 0 91 1071
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.89
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.065 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.351 33 5.5 %
Rwork0.354 562 -
obs--62 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

+
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