[English] 日本語
Yorodumi
- PDB-1cb9: NMR STRUCTURE WITH TIGHTLY BOUND WATER MOLECULES OF CYTOTOXIN II ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1cb9
TitleNMR STRUCTURE WITH TIGHTLY BOUND WATER MOLECULES OF CYTOTOXIN II (CARDIOTOXIN) FROM NAJA NAJA OXIANA IN AQUEOUS SOLUTION (MAJOR FORM).
ComponentsPROTEIN (CYTOTOXIN 2)
KeywordsTOXIN / CYTOXIN (CARDIOTOXIN) / MEMBRANE PERTURBATION / CIS/TRANS ISOMERIZATION / BOUND WATER
Function / homology
Function and homology information


other organism cell membrane / toxin activity / killing of cells of another organism / extracellular region / membrane
Similarity search - Function
Snake cytotoxin, cobra-type / Snake three-finger toxin / Snake toxins signature. / Snake toxin, conserved site / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesNaja oxiana (Central Asian cobra)
MethodSOLUTION NMR / SIMULATED ANNEALING BY MOLECULAR DYNAMICS IN TORSION ANGLE SPACE
AuthorsDementieva, D.V. / Bocharov, E.V. / Arseniev, A.S.
Citation
Journal: Eur.J.Biochem. / Year: 1999
Title: Two forms of cytotoxin II (cardiotoxin) from Naja naja oxiana in aqueous solution: spatial structures with tightly bound water molecules.
Authors: Dementieva, D.V. / Bocharov, E.V. / Arseniev, A.S.
#1: Journal: RUSS.J.BIOORGANIC CHEM. / Year: 1996
Title: Secondary Structure and Conformational Heterogeneity of Cytotoxin II from Naja Naja Oxiana
Authors: Dementieva, D.V. / Utkin Yu, N. / Arseniev, A.S.
History
DepositionMar 1, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jun 29, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (CYTOTOXIN 2)


Theoretical massNumber of molelcules
Total (without water)6,6481
Polymers6,6481
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 220LEAST RESTRAINT VIOLATION (TARGET FUNCTION VALUE)
Representative

-
Components

#1: Protein PROTEIN (CYTOTOXIN 2)


Mass: 6648.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Naja oxiana (Central Asian cobra) / Secretion: VENOM / References: UniProt: P01441
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111COSY
121TOCSY
131NOESY
141ROESY
NMR detailsText: THE STRUCTURE WAS DETERMINED BY HOMONUCLEAR NMR SPECTROSCOPY, USING GRADIENT TECHNIQUE. ROESY EXPERIMENTS WERE HELD AT 290 AND 318K.

-
Sample preparation

DetailsContents: 90% WATER/10% D2O; 100% D2O
Sample conditionspH: 5.5 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Varian UNITY 600 / Manufacturer: Varian / Model: UNITY 600 / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
FANTOM4FRACZKIEWICZ, MUMENTHALER, FREYBERG, SCHAUMANNrefinement
VARIAN VNMRVNMRstructure solution
XEASYstructure solution
DYANAstructure solution
RefinementMethod: SIMULATED ANNEALING BY MOLECULAR DYNAMICS IN TORSION ANGLE SPACE
Software ordinal: 1
Details: THE RESTRAINED REFINMENT WAS MADE IN VACUUM AND ONLY FOR PROTEIN SIDE CHAINS.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION (TARGET FUNCTION VALUE)
Conformers calculated total number: 220 / Conformers submitted total number: 20

+
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