[English] 日本語
Yorodumi
- PDB-1dm0: SHIGA TOXIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1dm0
TitleSHIGA TOXIN
Components
  • SHIGA TOXIN A SUBUNIT
  • SHIGA TOXIN B SUBUNIT
KeywordsTOXIN / AB5 STRUCTURE / POLYPEPTIDE A / BLOCKING / ACTIVE SITE
Function / homology
Function and homology information


hemolysis by symbiont of host erythrocytes / rRNA N-glycosylase / rRNA N-glycosylase activity / metabolic process / toxin activity / negative regulation of translation / extracellular region
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #70 / Shiga-like toxin, subunit A / Shiga-like toxin, beta subunit / Shiga-like toxin beta subunit / Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Enterotoxin / Ribosome-inactivating protein conserved site ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #70 / Shiga-like toxin, subunit A / Shiga-like toxin, beta subunit / Shiga-like toxin beta subunit / Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Enterotoxin / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily / Ribosome inactivating protein / Few Secondary Structures / Irregular / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Shiga toxin subunit B / rRNA N-glycosylase / Shiga toxin subunit A
Similarity search - Component
Biological speciesShigella dysenteriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsFraser, M.E. / Chernaia, M.M. / Kozlov, Y.V. / James, M.N.
Citation
Journal: Nat.Struct.Biol. / Year: 1994
Title: Crystal structure of the holotoxin from Shigella dysenteriae at 2.5 A resolution.
Authors: Fraser, M.E. / Chernaia, M.M. / Kozlov, Y.V. / James, M.N.
#1: Journal: Protein Toxin Structure, Parker, M.W., Ed. / Year: 1996
Title: X-ray Crystal Structure of the Shiga Toxin
Authors: Fraser, M.E. / Chernaia, M.M. / Kozlov, Y.V. / James, M.N.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Purification and Crystallization of Shiga Toxin from Shigella dysenteriae
Authors: Kozlov, Y.V. / Chernaia, M.M. / Fraser, M.E. / James, M.N.
History
DepositionDec 13, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Aug 14, 2019Group: Data collection / Category: computing

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SHIGA TOXIN A SUBUNIT
L: SHIGA TOXIN A SUBUNIT
B: SHIGA TOXIN B SUBUNIT
C: SHIGA TOXIN B SUBUNIT
D: SHIGA TOXIN B SUBUNIT
E: SHIGA TOXIN B SUBUNIT
F: SHIGA TOXIN B SUBUNIT
G: SHIGA TOXIN B SUBUNIT
H: SHIGA TOXIN B SUBUNIT
I: SHIGA TOXIN B SUBUNIT
J: SHIGA TOXIN B SUBUNIT
K: SHIGA TOXIN B SUBUNIT


Theoretical massNumber of molelcules
Total (without water)140,11012
Polymers140,11012
Non-polymers00
Water1,11762
1
A: SHIGA TOXIN A SUBUNIT
B: SHIGA TOXIN B SUBUNIT
C: SHIGA TOXIN B SUBUNIT
D: SHIGA TOXIN B SUBUNIT
E: SHIGA TOXIN B SUBUNIT
F: SHIGA TOXIN B SUBUNIT


Theoretical massNumber of molelcules
Total (without water)70,0556
Polymers70,0556
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8590 Å2
ΔGint-45 kcal/mol
Surface area23120 Å2
MethodPISA
2
L: SHIGA TOXIN A SUBUNIT
G: SHIGA TOXIN B SUBUNIT
H: SHIGA TOXIN B SUBUNIT
I: SHIGA TOXIN B SUBUNIT
J: SHIGA TOXIN B SUBUNIT
K: SHIGA TOXIN B SUBUNIT


Theoretical massNumber of molelcules
Total (without water)70,0556
Polymers70,0556
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8470 Å2
ΔGint-42 kcal/mol
Surface area23140 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21090 Å2
ΔGint-81 kcal/mol
Surface area42230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.050, 147.460, 83.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein SHIGA TOXIN A SUBUNIT


Mass: 31561.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella dysenteriae (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): HB101
References: UniProt: Q7BQ99, UniProt: Q9FBI2*PLUS, rRNA N-glycosylase
#2: Protein
SHIGA TOXIN B SUBUNIT


Mass: 7698.634 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella dysenteriae (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: Q7BQ98
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.91 Å3/Da / Density % sol: 57.68 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5
Details: sodium citrate, ethanol, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Details: Kozlov, Y.Z., (1993) J. Mol. Biol., 232, 704.

-
Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Oct 23, 1992
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→10 Å / Num. all: 47612 / Num. obs: 47612 / % possible obs: 83.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.5→2.67 Å / Num. unique all: 5446 / % possible all: 53.1
Reflection shell
*PLUS
% possible obs: 53.1 %

-
Processing

Software
NameClassification
TNTrefinement
BIOMOLdata reduction
BRUTEmodel building
MLPHAREphasing
DEMONmodel building
X-PLORrefinement
WEISdata scaling
WEISdata reduction
BIOMOLdata scaling
BRUTEphasing
DEMONphasing
RefinementResolution: 2.5→10 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: TNT dictionary / Details: Refinement with X-PLOR and TNT
RfactorNum. reflection% reflection
Rwork0.206 --
obs0.206 47612 83.1 %
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9476 0 0 62 9538
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.03
X-RAY DIFFRACTIONt_bond_d0.011
X-RAY DIFFRACTIONt_pseud_angle20.4
X-RAY DIFFRACTIONt_trig_c_planes0.007
X-RAY DIFFRACTIONt_gen_planes0.011
Software
*PLUS
Name: 'X-PLOR, TNT' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg20.4
X-RAY DIFFRACTIONx_plane_restr0.011

+
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