[English] 日本語
Yorodumi
- PDB-8u5e: Crystal Structure of C-terminal domain of Clostridium perfringens... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8u5e
TitleCrystal Structure of C-terminal domain of Clostridium perfringens Enterotoxin in Space Group P 21 21 21
ComponentsHeat-labile enterotoxin B chain
KeywordsTOXIN / HEAT-LABILE ENTEROTOXIN
Function / homologyClostridium enterotoxin / Clostridium enterotoxin / toxin activity / extracellular region / ACETATE ION / Heat-labile enterotoxin B chain
Function and homology information
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsKapoor, S. / Vecchio, A.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM138368 United States
CitationJournal: Toxins / Year: 2023
Title: Structural Basis of Clostridium perfringens Enterotoxin Activation and Oligomerization by Trypsin.
Authors: Ogbu, C.P. / Kapoor, S. / Vecchio, A.J.
History
DepositionSep 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heat-labile enterotoxin B chain
B: Heat-labile enterotoxin B chain
C: Heat-labile enterotoxin B chain
D: Heat-labile enterotoxin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,48525
Polymers62,7374
Non-polymers1,74821
Water12,124673
1
A: Heat-labile enterotoxin B chain
B: Heat-labile enterotoxin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,10211
Polymers31,3692
Non-polymers7349
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Heat-labile enterotoxin B chain
D: Heat-labile enterotoxin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,38314
Polymers31,3692
Non-polymers1,01412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.630, 64.000, 136.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Heat-labile enterotoxin B chain


Mass: 15684.372 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: cpe / Plasmid: pFastBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P01558
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 673 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.64 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 100 mM sodium acetate pH 4.5, 200 mM sodium chloride, and 1.0 M ammonium sulphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 20, 2016
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 1.4→59.187 Å / Num. obs: 186626 / % possible obs: 88.96 % / Redundancy: 2.19 % / CC1/2: 0.999 / Net I/σ(I): 9.55
Reflection shellResolution: 1.4→1.45 Å / Mean I/σ(I) obs: 0.29 / Num. unique obs: 5803 / CC1/2: 0.125

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDS0.82data reduction
pointlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→59.187 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2046 3571 1.94 %
Rwork0.1612 --
obs0.1621 183919 83.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→59.187 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3990 0 111 673 4774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034354
X-RAY DIFFRACTIONf_angle_d0.6425938
X-RAY DIFFRACTIONf_dihedral_angle_d16.0351590
X-RAY DIFFRACTIONf_chiral_restr0.073656
X-RAY DIFFRACTIONf_plane_restr0.003766
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.41850.4816380.43751955X-RAY DIFFRACTION24
1.4185-1.43790.3907430.43532350X-RAY DIFFRACTION28
1.4379-1.45840.4584510.40153256X-RAY DIFFRACTION39
1.4584-1.48020.4439750.38654057X-RAY DIFFRACTION49
1.4802-1.50330.3784870.36294859X-RAY DIFFRACTION59
1.5033-1.5280.4161040.34435530X-RAY DIFFRACTION66
1.528-1.55430.31571220.31186298X-RAY DIFFRACTION76
1.5543-1.58260.35771330.28246952X-RAY DIFFRACTION84
1.5826-1.6130.35461490.26757789X-RAY DIFFRACTION94
1.613-1.6460.29251700.25268205X-RAY DIFFRACTION99
1.646-1.68180.30231700.23888179X-RAY DIFFRACTION99
1.6818-1.72090.27871530.23298134X-RAY DIFFRACTION98
1.7209-1.76390.26681690.21958119X-RAY DIFFRACTION98
1.7639-1.81160.28521660.21237894X-RAY DIFFRACTION96
1.8116-1.86490.24921530.19438107X-RAY DIFFRACTION97
1.8649-1.92510.2271700.16788172X-RAY DIFFRACTION99
1.9251-1.99390.20211650.15668209X-RAY DIFFRACTION99
1.9939-2.07380.20631650.15128057X-RAY DIFFRACTION98
2.0738-2.16820.21011550.14827919X-RAY DIFFRACTION96
2.1682-2.28250.22541620.15078164X-RAY DIFFRACTION98
2.2825-2.42550.21171690.1498144X-RAY DIFFRACTION98
2.4255-2.61280.23741630.15138094X-RAY DIFFRACTION98
2.6128-2.87570.21521570.14877875X-RAY DIFFRACTION95
2.8757-3.29180.16941670.13458136X-RAY DIFFRACTION98
3.2918-4.14710.13141590.11897883X-RAY DIFFRACTION95
4.1471-59.1870.15631560.13588011X-RAY DIFFRACTION97

+
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://pdbjlvh1.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