[English] 日本語
Yorodumi
- PDB-6pnw: X-RAY STRUCTURE OF ERABUTOXIN C, A DIMERIC NEUROTOXIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6pnw
TitleX-RAY STRUCTURE OF ERABUTOXIN C, A DIMERIC NEUROTOXIN
ComponentsErabutoxin c
KeywordsTOXIN / NEUROTOXIN / SNAKE VENOM
Function / homology
Function and homology information


acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesLaticauda semifasciata (broad-banded blue sea krait)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCorfield, P.W.R. / Low, B.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS22719 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS07747 United States
Citation
Journal: AM.CRYST.ASSOC.,ABSTR.PAPERS (ANNUAL MEETING) / Year: 1992
Title: The Structure Of Erabutoxin C At 2.1A Resolution
Authors: Corfield, P.W.R. / Low, B.W.
Abstract: Scalar: PC53
#1: Journal: Acta Crystallogr.,Sect.B / Year: 1992
Title: Structure determination of a dimeric form of erabutoxin-b, crystallized from a thiocyanate solution.
Authors: Saludjian, P. / Prange, T. / Navaza, J. / Menez, R. / Guilloteau, J.P. / Ries-Kautt, M. / Ducruix, A.
History
DepositionJul 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700SHEET EACH OF THE TWO CRYSTALLOGRAPHICALLY INDEPENDENT MOLECULES HAS FIVE BETA STRANS A, B, C, D, E ...SHEET EACH OF THE TWO CRYSTALLOGRAPHICALLY INDEPENDENT MOLECULES HAS FIVE BETA STRANS A, B, C, D, E ARRANGED INTO TWO BETA SHEETS A,B AND C,D,E. THE TWO MOLECULES ARE LINKED VIA FOUR MAIN-CHAIN HYDROGEN BONDS BETWEEN LEU52, CYS54, AND GLU56 ON EACH MOLECULE, WITH A PSEUDO TWO-FOLD AXIS RELATING THE TWO MOLECULES PASSING BETWEEN THE TWO HYDROGEN BONDS LINING CYS54 ON EACH MOLECULE. THESE FOUR HYDROGEN BONDS LEAD TO AN EXTENDED SIX-CHAIN BETA SHEET IN THE DIMER.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Erabutoxin c
B: Erabutoxin c


Theoretical massNumber of molelcules
Total (without water)13,7252
Polymers13,7252
Non-polymers00
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-1 kcal/mol
Surface area7710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.600, 53.750, 40.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (-1), (1), (-1))

-
Components

#1: Protein Erabutoxin c / Ec / Short neurotoxin 1c


Mass: 6862.682 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Laticauda semifasciata (broad-banded blue sea krait)
Secretion: VENOM / References: UniProt: Q7T2I5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.87 %
Description: Long Rod, 0.25x0.35x1.5 mm; data collected on two halves
Crystal growTemperature: 298 K / Method: evaporation / pH: 6 / Details: PHOSPHATE BUFFER, AMMONIUM SULFATE PH 6 / PH range: 6

-
Data collection

DiffractionMean temperature: 290 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Details: Syntex P21 diffractometer / Wavelength: 1.542 Å
DetectorType: SYNTEX / Detector: DIFFRACTOMETER / Date: Feb 1, 1983 / Details: Syntex P21 diffractometer
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2→38 Å / Num. obs: 7681 / % possible obs: 85.6 % / Redundancy: 2.2 %
Details: Data processing used Bob Blessing's REFPK program for extracting intensities from the profiles, and his SORTAV for data merging. We did an empirical absorption correction based upon psi scans.
Rmerge(I) obs: 0.08 / Net I/σ(I): 7.3
Reflection shellResolution: 2→2.2 Å / Num. unique obs: 986 / % possible all: 70

-
Processing

Software
NameClassificationNB
PROLSQrefinement
REFPKdata processing
SORTAVdata scaling
SORTVAdata reduction
TFORMphasing
FRFSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3EBX, ERABUTOXIN B

3ebx


Resolution: 2→10 Å / Cross valid method: NONE / σ(F): 4
Details: R Value from Prolsq based upon 5798 reflections with F>4Sigma. No Rfree set. The two crystallographically independent molecules are related by a non-crystallographic two-fold axis which ...Details: R Value from Prolsq based upon 5798 reflections with F>4Sigma. No Rfree set. The two crystallographically independent molecules are related by a non-crystallographic two-fold axis which lies in the YZ plane, at an approximate angle of 35 degrees with the Z axis. The mtrix transformations below willl operate on coordinates of atoms in chain B to give coordinates close to those for corresponding aotms in chain A. MTRIX1 1 -0.99795 0.02380 0.05933 -8.84136, MTRIX2 1 0.06391 0.35231 0.93370 8.38409 MTRIX3 1 0.00133 0.93558 -0.35311 -11.71019. Rotation and translational searches were done with Crowther and Blow's suite of programs applied locally.
RfactorNum. reflection% reflectionSelection details
Rwork0.161 ---
obs-7469 85.6 %-
Rfree---NONE
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms948 0 0 145 1093

+
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