[English] 日本語
Yorodumi
- PDB-5lzj: Cholera toxin El Tor B-pentamer in complex with inhibitor Laura237 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lzj
TitleCholera toxin El Tor B-pentamer in complex with inhibitor Laura237
ComponentsCholera enterotoxin subunit B
KeywordsTOXIN / cholera toxin B-pentamer / inhibitor
Function / homology
Function and homology information


host cell surface binding / galactose binding / positive regulation of tyrosine phosphorylation of STAT protein / catalytic complex / toxin activity / periplasmic space / host cell plasma membrane / extracellular region / membrane
Similarity search - Function
Heat-labile enterotoxin, B chain / Heat-labile enterotoxin beta chain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-7BT / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Cholera enterotoxin subunit B
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsHeggelund, J.E. / Krengel, U.
CitationJournal: Sci Rep / Year: 2017
Title: Towards new cholera prophylactics and treatment: Crystal structures of bacterial enterotoxins in complex with GM1 mimics.
Authors: Heggelund, J.E. / Mackenzie, A. / Martinsen, T. / Benjamin Heim, J. / Cheshev, P. / Bernardi, A. / Krengel, U.
History
DepositionSep 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cholera enterotoxin subunit B
B: Cholera enterotoxin subunit B
C: Cholera enterotoxin subunit B
D: Cholera enterotoxin subunit B
E: Cholera enterotoxin subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,76512
Polymers58,3025
Non-polymers1,4647
Water9,890549
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13810 Å2
ΔGint-44 kcal/mol
Surface area21340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.245, 66.476, 82.401
Angle α, β, γ (deg.)90.00, 116.96, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 5 molecules ABCDE

#1: Protein
Cholera enterotoxin subunit B / Cholera enterotoxin B chain / Cholera enterotoxin gamma chain / Choleragenoid


Mass: 11660.348 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Gene: ctxB, toxB, VC_1456 / Production host: Vibrio sp. (bacteria) / References: UniProt: P01556

-
Non-polymers , 5 types, 556 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-7BT / (~{Z})-~{N}-[2-[(2~{R},3~{R},4~{R},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]ethyl]-3-(3,4,5-trimethoxyphenyl)prop-2-enamide / Laura237


Mass: 427.446 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29NO9
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 549 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES pH 6, 30% PEG 400, 3% PGA-LM

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97239 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97239 Å / Relative weight: 1
ReflectionResolution: 1.2→45.6 Å / Num. obs: 144269 / % possible obs: 93.8 % / Redundancy: 2.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.096 / Net I/σ(I): 5.55
Reflection shellResolution: 1.2→1.27 Å / Redundancy: 2.3 % / CC1/2: 0.337 / % possible all: 72.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CHB

3chb


Resolution: 1.2→73.45 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.441 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22817 7295 5.1 %RANDOM
Rwork0.19506 ---
obs0.19671 136978 93.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.371 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å20.02 Å2
2---0.64 Å20 Å2
3---0.96 Å2
Refinement stepCycle: 1 / Resolution: 1.2→73.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4085 0 99 549 4733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.024444
X-RAY DIFFRACTIONr_bond_other_d0.0030.024378
X-RAY DIFFRACTIONr_angle_refined_deg2.1541.9666027
X-RAY DIFFRACTIONr_angle_other_deg1.1443.00410142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0945566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.16925.567194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4115849
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.3491515
X-RAY DIFFRACTIONr_chiral_restr0.1290.2693
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024915
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02964
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7641.4892111
X-RAY DIFFRACTIONr_mcbond_other1.7531.4872110
X-RAY DIFFRACTIONr_mcangle_it2.6812.2252644
X-RAY DIFFRACTIONr_mcangle_other2.6812.2262645
X-RAY DIFFRACTIONr_scbond_it2.3951.8312333
X-RAY DIFFRACTIONr_scbond_other2.3921.8312329
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6662.6353350
X-RAY DIFFRACTIONr_long_range_B_refined5.34219.0365086
X-RAY DIFFRACTIONr_long_range_B_other5.34119.0345086
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.199→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 360 -
Rwork0.383 6801 -
obs--63.23 %

+
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