[English] 日本語
Yorodumi
- PDB-1uyj: Clostridium perfringens epsilon toxin shows structural similarity... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1uyj
TitleClostridium perfringens epsilon toxin shows structural similarity with the pore forming toxin aerolysin
ComponentsEPSILON-TOXIN
KeywordsTOXIN / BETA PORE FORMING TOXIN
Function / homology
Function and homology information


Dihydrodipicolinate Reductase; domain 2 - #60 / Epsilon toxin / Proaerolysin, chain A, domain 3 / Aerolysin-like toxin / Clostridium epsilon toxin ETX/Bacillus mosquitocidal toxin MTX2 / Proaerolysin; Chain A, domain 3 / Dihydrodipicolinate Reductase; domain 2 / Beta Complex / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
URANIUM ATOM / Epsilaon-toxin
Similarity search - Component
Biological speciesCLOSTRIDIUM PERFRINGENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsCole, A.R. / Gibert, M. / Poppoff, M. / Moss, D.S. / Titball, R.W. / Basak, A.K.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Clostridium Perfringens Epsilon-Toxin Shows Structural Similarity to the Pore-Forming Toxin Aerolysin
Authors: Cole, A.R. / Gibert, M. / Popoff, M. / Moss, D.S. / Titball, R.W. / Basak, A.K.
History
DepositionMar 2, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2004Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EPSILON-TOXIN
B: EPSILON-TOXIN
C: EPSILON-TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,90415
Polymers99,0473
Non-polymers2,85612
Water93752
1
A: EPSILON-TOXIN
hetero molecules

A: EPSILON-TOXIN
hetero molecules

A: EPSILON-TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,19012
Polymers99,0473
Non-polymers2,1429
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_765-x+y+2,-x+1,z1
crystal symmetry operation2_645-y+1,x-y-1,z1
MethodPQS
2
B: EPSILON-TOXIN
hetero molecules

B: EPSILON-TOXIN
hetero molecules

B: EPSILON-TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,61818
Polymers99,0473
Non-polymers3,57015
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
MethodPQS
3
C: EPSILON-TOXIN
hetero molecules

C: EPSILON-TOXIN
hetero molecules

C: EPSILON-TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,90415
Polymers99,0473
Non-polymers2,85612
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)125.962, 125.962, 121.862
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-2010-

HOH

21B-2012-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1, 0.018, -0.002), (-0.018, 1, -0.019), (0.002, 0.019, 1)-125.0723, 77.71906, -122.35224
2given(0.507, -0.862, 0.01), (-0.862, -0.507, 0.005), (0.001, -0.011, -1)-2.06325, 143.94244, 166.96523
DetailsALTHOUGH IN THE CRYSTAL THE MOLECULE IS A TRIMER THISIS CRYSTALLOGRAPHIC AND NOT RELEVANT BIOLOGICALLY

-
Components

#1: Protein EPSILON-TOXIN


Mass: 33015.793 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) CLOSTRIDIUM PERFRINGENS (bacteria) / Variant: TOXINOTYPE D / References: UniProt: Q57398
#2: Chemical
ChemComp-U1 / URANIUM ATOM


Mass: 238.029 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: U
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 51.6 %
Crystal growpH: 7 / Details: 25% ETHYLENE GLYCOL, pH 7.00

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.77, 1.653, 0.885
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 15, 2002 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.771
21.6531
30.8851
ReflectionResolution: 2.6→55.9 Å / Num. obs: 33253 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 8.91 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 10.0438
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 8.85 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 2.8 / % possible all: 97.2

-
Processing

Software
NameClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
SHARPphasing
REFMACrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.6→50 Å / SU B: 12.163 / SU ML: 0.261 / Cross valid method: THROUGHOUT / ESU R Free: 0.342
Details: THE N-TERMINAL 15 RESIDUES ARE DISORDERED, RESIDUES 273 - 279 APPEARED DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.29006 1683 5 %RANDOM
Rwork0.23631 ---
obs0.23905 31967 98.34 %-
Displacement parametersBiso mean: 45.909 Å2
Baniso -1Baniso -2Baniso -3
1-1.16 Å20.58 Å20 Å2
2--1.16 Å20 Å2
3----1.74 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6256 0 12 52 6320

+
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