[English] 日本語
Yorodumi
- PDB-7vd7: Toxin - Antitoxin complex from Salmonella enterica serovar Typhimurium -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vd7
TitleToxin - Antitoxin complex from Salmonella enterica serovar Typhimurium
Components
  • antitoxin
  • toxin
KeywordsTOXIN/ANTITOXIN / Toxin-Antitoxin complex Ribonuclease / TOXIN / TOXIN-ANTITOXIN complex
Function / homology
Function and homology information


BrnA antitoxin of type II toxin-antitoxin system / BrnA antitoxin of type II toxin-antitoxin system / Ribonuclease toxin, BrnT, of type II toxin-antitoxin system / Ribonuclease toxin, BrnT, of type II toxin-antitoxin system / Ribonuclease toxin BrnT superfamily / Ribonuclease toxin, BrnT, of type II toxin-antitoxin system / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
BrnT family toxin / BrnA antitoxin family protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsEun, H.-J. / Lee, B.-J. / Jang, S.-W. / Park, J.-H.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2018R1A5A2024425 Korea, Republic Of
National Research Foundation (NRF, Korea)2021R1F1A1050961 Korea, Republic Of
National Research Foundation (NRF, Korea)2021 BK21 Plus Project for Medicine, Dentistry and Pharmacy Korea, Republic Of
CitationJournal: To Be Published
Title: Toxin-Antitoxin complex from Salmonella enterica serovar Typhimurium
Authors: Eun, H.-J. / Jang, S.-W. / Park, J.-H. / Lee, B.-J.
History
DepositionSep 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: toxin
B: antitoxin


Theoretical massNumber of molelcules
Total (without water)16,1152
Polymers16,1152
Non-polymers00
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-14 kcal/mol
Surface area7550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.366, 31.605, 47.985
Angle α, β, γ (deg.)90.00, 90.63, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein toxin / BrnT family toxin / Membrane protein / Putative inner membrane protein / Ribonuclease toxin / BrnT ...BrnT family toxin / Membrane protein / Putative inner membrane protein / Ribonuclease toxin / BrnT / of type II toxin-antitoxin system


Mass: 11171.613 Da / Num. of mol.: 1 / Mutation: E74D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: 14028s / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F7JD05
#2: Protein/peptide antitoxin / BrnA antitoxin family protein / BrnA antitoxin of type II toxin-antitoxin system / Putative ...BrnA antitoxin family protein / BrnA antitoxin of type II toxin-antitoxin system / Putative cytoplasmic protein / Toxin-antitoxin system / antitoxin component


Mass: 4943.373 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F7JDL4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 1.85 Å3/Da / Density % sol: 33.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 6000 100 mM HEPES/ Sodium hydroxide pH 7.0 200 mM Sodium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97959 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97959 Å / Relative weight: 1
ReflectionResolution: 1.42→50 Å / Num. obs: 20736 / % possible obs: 93.13 % / Redundancy: 6.4 % / Biso Wilson estimate: 16.68 Å2 / CC1/2: 0.999 / Net I/σ(I): 49.02
Reflection shellResolution: 1.42→1.46 Å / Redundancy: 5.7 % / Num. unique obs: 1569 / CC1/2: 0.975

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.19.2-4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: no PDB entry

Resolution: 1.43→24 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.323 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21615 1054 5.1 %RANDOM
Rwork0.19561 ---
obs0.19664 19672 93.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.872 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å2-0 Å21.15 Å2
2--0.84 Å20 Å2
3----0.47 Å2
Refinement stepCycle: 1 / Resolution: 1.43→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1137 0 0 145 1282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131162
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181080
X-RAY DIFFRACTIONr_angle_refined_deg1.731.6431560
X-RAY DIFFRACTIONr_angle_other_deg1.4821.5952478
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2265136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.96820.61781
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.34415205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9531514
X-RAY DIFFRACTIONr_chiral_restr0.0950.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021320
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02300
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_it2.1061.895550
X-RAY DIFFRACTIONr_mcbond_other2.0721.891549
X-RAY DIFFRACTIONr_mcangle_it2.9522.835684
X-RAY DIFFRACTIONr_mcangle_other2.9542.838685
X-RAY DIFFRACTIONr_scbond_it3.2532.296612
X-RAY DIFFRACTIONr_scbond_other3.252.297613
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8853.301877
X-RAY DIFFRACTIONr_long_range_B_refined6.36324.3591349
X-RAY DIFFRACTIONr_long_range_B_other6.33823.8381322
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.43→1.464 Å
RfactorNum. reflection% reflection
Rfree0.314 84 -
Rwork0.247 1475 -
obs--95.94 %

+
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