[English] 日本語
Yorodumi
- PDB-8ow8: Crystal Structure of the Catalytic Domain of a Botulinum Neurotox... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ow8
TitleCrystal Structure of the Catalytic Domain of a Botulinum Neurotoxin Homologue from Enterococcus faecium
ComponentsBotulinum-like toxin eBoNT/J light chain
KeywordsTOXIN / Botulinum neurotoxin / homologue / enterococcus faecium
Function / homology
Function and homology information


bontoxilysin / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / host cell cytoplasmic vesicle membrane / toxin activity / host cell plasma membrane / proteolysis / extracellular region / zinc ion binding / membrane
Similarity search - Function
Botulinum neurotoxin, helical domain / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / PHOSPHATE ION / Botulinum-like toxin eBoNT/J
Similarity search - Component
Biological speciesEnterococcus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGregory, K.S. / Acharya, K.R. / Liu, S.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int J Mol Sci / Year: 2023
Title: Crystal Structure of the Catalytic Domain of a Botulinum Neurotoxin Homologue from Enterococcus faecium : Potential Insights into Substrate Recognition.
Authors: Gregory, K.S. / Hall, P.R. / Onuh, J.P. / Mojanaga, O.O. / Liu, S.M. / Acharya, K.R.
History
DepositionApr 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Botulinum-like toxin eBoNT/J light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2116
Polymers50,7441
Non-polymers4685
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-49 kcal/mol
Surface area18010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.894, 143.894, 51.695
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Botulinum-like toxin eBoNT/J light chain / LC


Mass: 50743.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus (bacteria) / Gene: A5816_002916 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A242DI27, bontoxilysin

-
Non-polymers , 5 types, 161 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.35 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M SPG (succinic acid, sodium phosphate monobasic monohydrate, and glycine) buffer pH 7.0, 25% w/v PEG 1500

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→143.89 Å / Num. obs: 37319 / % possible obs: 100 % / Redundancy: 26.3 % / CC1/2: 1 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.036 / Rrim(I) all: 0.134 / Net I/σ(I): 13.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 26.6 % / Rmerge(I) obs: 3.807 / Num. unique obs: 2683 / CC1/2: 0.626 / Rpim(I) all: 1.06 / Rrim(I) all: 3.952

-
Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
REFMAC5.8.0419refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→64.434 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.21 / WRfactor Rwork: 0.177 / SU B: 10.517 / SU ML: 0.139 / Average fsc free: 0.951 / Average fsc work: 0.9613 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.141
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2237 1882 5.051 %RANDOM
Rwork0.1883 35375 --
all0.19 ---
obs-37257 99.944 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 55.903 Å2
Baniso -1Baniso -2Baniso -3
1-1.266 Å2-0 Å20 Å2
2--1.266 Å20 Å2
3----2.532 Å2
Refinement stepCycle: LAST / Resolution: 2→64.434 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3218 0 25 156 3399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123319
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163151
X-RAY DIFFRACTIONr_angle_refined_deg1.911.6594489
X-RAY DIFFRACTIONr_angle_other_deg0.6061.5787285
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4495401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.224513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.22610593
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.23210156
X-RAY DIFFRACTIONr_chiral_restr0.0850.2497
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023804
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02734
X-RAY DIFFRACTIONr_nbd_refined0.2260.2654
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.23022
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21674
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.21809
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2164
X-RAY DIFFRACTIONr_metal_ion_refined0.2080.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0930.217
X-RAY DIFFRACTIONr_nbd_other0.1970.261
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.190.24
X-RAY DIFFRACTIONr_mcbond_it3.9123.8081604
X-RAY DIFFRACTIONr_mcbond_other3.9123.8081604
X-RAY DIFFRACTIONr_mcangle_it5.276.8222002
X-RAY DIFFRACTIONr_mcangle_other5.2696.8252003
X-RAY DIFFRACTIONr_scbond_it4.9044.1761715
X-RAY DIFFRACTIONr_scbond_other4.9034.1781716
X-RAY DIFFRACTIONr_scangle_it6.6717.4832486
X-RAY DIFFRACTIONr_scangle_other6.677.4842487
X-RAY DIFFRACTIONr_lrange_it8.20736.4533720
X-RAY DIFFRACTIONr_lrange_other8.20736.4583721
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2-2.0520.3491410.33825340.33926810.90.89599.77620.339
2.052-2.1080.3071140.31425200.31326350.9060.91199.96210.311
2.108-2.1690.2751420.28224210.28225630.9440.9351000.277
2.169-2.2360.2541190.2424040.24125230.9520.9561000.23
2.236-2.3090.271290.22822760.23124060.9550.96399.95840.216
2.309-2.390.3041130.21922380.22323520.9490.96899.95750.205
2.39-2.480.2791050.2221750.22322810.9540.97299.95620.201
2.48-2.5810.3081120.21920760.22321890.9430.97299.95430.199
2.581-2.6960.326970.21619870.22120840.9420.9731000.197
2.696-2.8270.249830.20519500.20720340.9630.97799.95080.186
2.827-2.980.266950.21318120.21619070.9470.9731000.197
2.98-3.160.281040.21317310.21718350.9520.9721000.2
3.16-3.3770.255920.22316170.22517090.9660.9741000.214
3.377-3.6470.231920.20115320.20316240.9690.9821000.196
3.647-3.9940.19850.17814110.17914960.9770.9861000.174
3.994-4.4630.177720.13412770.13613490.9830.991000.132
4.463-5.150.157570.11311600.11512170.990.9931000.113
5.15-6.2970.168390.1529970.15310360.9840.9881000.152
6.297-8.8630.186580.1497830.1518410.9810.9881000.15
8.863-64.4340.188330.2114740.215090.980.96299.60710.215
Refinement TLS params.Method: refined / Origin x: 43.8046 Å / Origin y: -16.8654 Å / Origin z: 18.0325 Å
111213212223313233
T0.118 Å2-0.0687 Å20.0178 Å2-0.1724 Å20.0013 Å2--0.0176 Å2
L1.4734 °2-0.3734 °2-0.357 °2-1.3435 °20.1597 °2--1.5572 °2
S-0.0343 Å °-0.13 Å °-0.0447 Å °0.0554 Å °0.0282 Å °-0.0825 Å °0.1118 Å °0.3045 Å °0.0061 Å °
Refinement TLS groupSelection: ALL

+
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