[English] 日本語
Yorodumi
- PDB-1xtc: CHOLERA TOXIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1xtc
TitleCHOLERA TOXIN
Components(CHOLERA TOXIN) x 3
KeywordsTOXIN / ENTEROTOXIN
Function / homology
Function and homology information


host cell surface binding / galactose binding / positive regulation of tyrosine phosphorylation of STAT protein / glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / catalytic complex / nucleotidyltransferase activity / toxin activity / periplasmic space / lipid binding ...host cell surface binding / galactose binding / positive regulation of tyrosine phosphorylation of STAT protein / glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / catalytic complex / nucleotidyltransferase activity / toxin activity / periplasmic space / lipid binding / host cell plasma membrane / extracellular space / extracellular region / membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #240 / Heat-labile enterotoxin, A chain / Heat-labile enterotoxin alpha chain / Heat-Labile Enterotoxin; Chain A / Heat-Labile Enterotoxin, subunit A / Heat-labile enterotoxin, B chain / Heat-labile enterotoxin beta chain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #240 / Heat-labile enterotoxin, A chain / Heat-labile enterotoxin alpha chain / Heat-Labile Enterotoxin; Chain A / Heat-Labile Enterotoxin, subunit A / Heat-labile enterotoxin, B chain / Heat-labile enterotoxin beta chain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Complex / Up-down Bundle / Beta Barrel / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Cholera enterotoxin subunit A / Cholera enterotoxin subunit B
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsZhang, R.-G. / Westbrook, E.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: The three-dimensional crystal structure of cholera toxin.
Authors: Zhang, R.G. / Scott, D.L. / Westbrook, M.L. / Nance, S. / Spangler, B.D. / Shipley, G.G. / Westbrook, E.M.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: The 2.4 A Crystal Structure of Cholera Toxin B Subunit Pentamer: Choleragenoid
Authors: Zhang, R.G. / Westbrook, M.L. / Westbrook, E.M. / Scott, D.L. / Otwinowski, Z. / Maulik, P.R. / Reed, R.A. / Shipley, G.G.
History
DepositionJan 10, 1996Processing site: BNL
Revision 1.0Aug 1, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CHOLERA TOXIN
C: CHOLERA TOXIN
D: CHOLERA TOXIN
E: CHOLERA TOXIN
F: CHOLERA TOXIN
G: CHOLERA TOXIN
H: CHOLERA TOXIN


Theoretical massNumber of molelcules
Total (without water)85,7097
Polymers85,7097
Non-polymers00
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19330 Å2
ΔGint-67 kcal/mol
Surface area27960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.000, 92.200, 60.600
Angle α, β, γ (deg.)90.00, 106.40, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein CHOLERA TOXIN / CTX / CHOLERAGEN


Mass: 21841.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: COMMERCIALLY OBTAINED FROM LIST BIOLOGICAL LABORATORY, CAMPBER CA95008
Source: (natural) Vibrio cholerae (bacteria) / Strain: 569B / References: UniProt: P01555
#2: Protein/peptide CHOLERA TOXIN / CTX / CHOLERAGEN


Mass: 5404.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: COMMERCIALLY OBTAINED FROM LIST BIOLOGICAL LABORATORY, CAMPBER CA95008
Source: (natural) Vibrio cholerae (bacteria) / Strain: 569B / References: UniProt: P01555
#3: Protein
CHOLERA TOXIN / CTX / CHOLERAGEN


Mass: 11692.346 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Details: COMMERCIALLY OBTAINED FROM LIST BIOLOGICAL LABORATORY, CAMPBER CA95008
Source: (natural) Vibrio cholerae (bacteria) / Strain: 569B / References: UniProt: P01556
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHOLERA TOXIN CONTAINS 3 KINDS OF CHAINS: AN ALPHA AND A GAMMA CHAIN (FROM THE SAME PRECURSOR ...CHOLERA TOXIN CONTAINS 3 KINDS OF CHAINS: AN ALPHA AND A GAMMA CHAIN (FROM THE SAME PRECURSOR MOLECULE), LINKED BY AN INTERCHAIN DISULFIDE BOND, ASSOCIATED NONCOVALENTLY WITH AN AGGREGATE OF 4 TO 6 BETA CHAINS. CHAIN A IS THE A1 OR ALPHA CHAIN, CHAIN C IS THE A2 OR GAMMA CHAIN, AND CHAINS D, E, F, G, AND H ARE THE FIVE ASSOCIATED BETA CHAINS.
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal grow
*PLUS
Method: other / Details: Spangler, B.D., (1989) Biochemistry, 28, 1333.

-
Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Aug 15, 1989
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 26200 / % possible obs: 88.4 % / Rmerge(I) obs: 0.048
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. measured all: 60810 / Rmerge(I) obs: 0.048

-
Processing

Software
NameClassification
XENGENdata collection
X-PLORmodel building
PROFFTrefinement
X-PLORrefinement
XENGENdata reduction
X-PLORphasing
RefinementHighest resolution: 2.4 Å / σ(F): 1.5 /
RfactorNum. reflection
Rwork0.185 -
obs-26200
Displacement parametersBiso mean: 20.37 Å2
Refinement stepCycle: LAST / Highest resolution: 2.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5997 0 0 138 6135
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0320.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0450.06
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor obs: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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