[English] 日本語
Yorodumi
- PDB-7bwf: YoeB-YefM complex from Staphylococcus aureus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7bwf
TitleYoeB-YefM complex from Staphylococcus aureus
Components
  • (Antitoxin) x 2
  • Addiction module antitoxin RelB
KeywordsTOXIN/ANTITOXIN / Toxin-Antitoxin complex ribosome-dependent ribonuclease ribosome-independent ribonuclease Toxin inhibitor / TOXIN / TOXIN-ANTITOXIN complex
Function / homology
Function and homology information


RNA catabolic process / endonuclease activity
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #330 / YefM-like domain / Toxin YoeB / YoeB-like toxin of bacterial type II toxin-antitoxin system / Type II toxin-antitoxin system, antitoxin Phd/YefM / Antitoxin Phd_YefM, type II toxin-antitoxin system / YefM-like superfamily / YefM-like fold / RelE-like / Toxin-antitoxin system, RelE/ParE toxin family ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #330 / YefM-like domain / Toxin YoeB / YoeB-like toxin of bacterial type II toxin-antitoxin system / Type II toxin-antitoxin system, antitoxin Phd/YefM / Antitoxin Phd_YefM, type II toxin-antitoxin system / YefM-like superfamily / YefM-like fold / RelE-like / Toxin-antitoxin system, RelE/ParE toxin family / YaeB-like fold / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Antitoxin / Putative mRNA interferase YoeB
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLee, B.-J. / Eun, H.-J.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2018R1A2A1A19018526 Korea, Republic Of
National Research Foundation (NRF, Korea)2018R1A5A2024425 Korea, Republic Of
National Research Foundation (NRF, Korea)2019 BK21 Plus Project for Medicine, Dentistry and Pharmacy Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Crystal structure of the YoeBSa1-YefMSa1 complex from Staphylococcus aureus.
Authors: Eun, H.-J. / Lee, K.-Y. / Kim, D.-G. / Im, D.S. / Lee, B.-J.
History
DepositionApr 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Addiction module antitoxin RelB
B: Antitoxin
C: Addiction module antitoxin RelB
D: Antitoxin


Theoretical massNumber of molelcules
Total (without water)41,2364
Polymers41,2364
Non-polymers00
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Pull-down assay with hexahistidine tag
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10770 Å2
ΔGint-58 kcal/mol
Surface area16980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.849, 67.849, 69.356
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

-
Components

#1: Protein Addiction module antitoxin RelB / Addiction module toxin Txe/YoeB family protein


Mass: 10325.804 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: M1K003_0948, SAKG03_24000 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon plus / References: UniProt: A0A3A3ATA4
#2: Protein Antitoxin


Mass: 10335.587 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: yefM, BTN44_14530, EP54_09735, EQ90_00255, HMPREF3211_00052, M1K003_0949, NCTC10654_02579, NCTC10702_03766, NCTC5664_01444, NCTC6133_03236, NCTC7988_02488, RK64_12840, SAKG03_24010
Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon plus / References: UniProt: A0A0B4ND47
#3: Protein Antitoxin


Mass: 10248.509 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: yefM, BTN44_14530, EP54_09735, EQ90_00255, HMPREF3211_00052, M1K003_0949, NCTC10654_02579, NCTC10702_03766, NCTC5664_01444, NCTC6133_03236, NCTC7988_02488, RK64_12840, SAKG03_24010
Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon plus / References: UniProt: A0A0B4ND47
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.24 Å3/Da / Density % sol: 44.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.08 M sodium chloride, 0.02 M magnesium chloride hexahydrate, 0.04 M sodium cacodylate trihydrate pH 7.0, 40% v/v (+/-)-2-methyl-2,4-pentanediol, and 0.012 M spermine tetrahydrochloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 38302 / % possible obs: 97.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 26.9
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1944 / % possible all: 99

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A6Q

2a6q


Resolution: 1.7→44.832 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 26.31
RfactorNum. reflection% reflection
Rfree0.2296 2077 5.43 %
Rwork0.2056 --
obs0.207 38271 97.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 124.07 Å2 / Biso mean: 43.0848 Å2 / Biso min: 18.4 Å2
Refinement stepCycle: final / Resolution: 1.7→44.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2886 0 0 174 3060
Biso mean---40.94 -
Num. residues----357
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.73930.35221400.3066244499
1.7393-1.78280.27511740.2751242799
1.7828-1.8310.3195960.272252299
1.831-1.88490.29611310.2647243399
1.8849-1.94570.29511320.2631244399
1.9457-2.01530.30991360.2458240498
2.0153-2.0960.25971520.2497244498
2.096-2.19140.2711510.238242998
2.1914-2.30690.27361210.2183242498
2.3069-2.45140.25121470.2101237497
2.4514-2.64070.2251540.2106236096
2.6407-2.90640.24031340.2095237596
2.9064-3.32680.21851340.2039238596
3.3268-4.1910.20331150.1789238595
4.191-44.8320.19051600.1728234596
Refinement TLS params.Method: refined / Origin x: 17.3212 Å / Origin y: 9.135 Å / Origin z: 10.9917 Å
111213212223313233
T0.1336 Å2-0.0247 Å20.0174 Å2-0.1629 Å20.0087 Å2--0.1652 Å2
L1.1713 °20.3783 °20.6047 °2-0.8135 °20.3984 °2--1.4593 °2
S0.0521 Å °-0.0354 Å °-0.045 Å °-0.0221 Å °0.0906 Å °-0.0394 Å °0.0046 Å °0.0049 Å °-0.1225 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 88
2X-RAY DIFFRACTION1allB-8 - 83
3X-RAY DIFFRACTION1allC2 - 88
4X-RAY DIFFRACTION1allD-7 - 83
5X-RAY DIFFRACTION1allS1 - 238

+
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