[English] 日本語
Yorodumi
- PDB-6l8g: High resolution structure of YoeB in complex with YefM C-terminus... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6l8g
TitleHigh resolution structure of YoeB in complex with YefM C-terminus(46N-83V) from Staphylococcus aureus.
Components
  • Antitoxin
  • YoeB
KeywordsANTITOXIN/TOXIN / toxin-antitoxin / microbial RNase / YoeB / TOXIN / ANTITOXIN-TOXIN complex
Function / homology
Function and homology information


RNA catabolic process / endonuclease activity / negative regulation of DNA-templated transcription
Similarity search - Function
: / 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 / Toxin-antitoxin system, RelE/ParE toxin domain superfamily
Similarity search - Domain/homology
Antitoxin / Putative mRNA interferase YoeB
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsYue, J. / Xue, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of ChinaU1632124 to L.N. China
CitationJournal: To Be Published
Title: Structural insight into the mechanism of conditional cooperativity in the YoeB-YefM toxin-antitoxin system
Authors: Xue, L. / Yue, J.
History
DepositionNov 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Antitoxin
B: YoeB


Theoretical massNumber of molelcules
Total (without water)14,7652
Polymers14,7652
Non-polymers00
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-17 kcal/mol
Surface area6720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.206, 58.117, 65.597
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein/peptide Antitoxin


Mass: 4306.786 Da / Num. of mol.: 1 / Fragment: C-terminus
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / Gene: SAOUHSC_02692 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2G285
#2: Protein YoeB


Mass: 10457.985 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / Gene: SAOUHSC_02691 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2G286
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.03 Å3/Da / Density % sol: 39.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 5% v/v Tacsimate pH 7.0 0.1 M HEPES pH 7.0 10% w/v Polyethylene glycol monomethyl ether 5,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1→50 Å / Num. obs: 64910 / % possible obs: 99.3 % / Redundancy: 11.8 % / Biso Wilson estimate: 6.12 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.011 / Rrim(I) all: 0.04 / Net I/σ(I): 61.6
Reflection shellResolution: 1→1.02 Å / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 12.9 / Num. unique obs: 3023 / CC1/2: 0.996 / Rpim(I) all: 0.063 / Rrim(I) all: 0.187

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1→43.5 Å / SU ML: 0.0847 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 14.5732
RfactorNum. reflection% reflection
Rfree0.1758 3248 5.01 %
Rwork0.1679 --
obs0.1683 64824 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 8.5 Å2
Refinement stepCycle: LAST / Resolution: 1→43.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1022 0 0 177 1199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00391039
X-RAY DIFFRACTIONf_angle_d0.75431395
X-RAY DIFFRACTIONf_chiral_restr0.0783150
X-RAY DIFFRACTIONf_plane_restr0.0047181
X-RAY DIFFRACTIONf_dihedral_angle_d13.1342402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.010.22661250.24422423X-RAY DIFFRACTION91.39
1.01-1.030.18961520.2042617X-RAY DIFFRACTION98.79
1.03-1.050.18961490.17492644X-RAY DIFFRACTION99.86
1.05-1.070.17131340.15822681X-RAY DIFFRACTION99.82
1.07-1.080.15211210.15152656X-RAY DIFFRACTION99.25
1.08-1.110.15411370.14212647X-RAY DIFFRACTION99.25
1.11-1.130.11661350.14132638X-RAY DIFFRACTION99.6
1.13-1.150.15571470.14172690X-RAY DIFFRACTION99.89
1.15-1.180.13331400.14462647X-RAY DIFFRACTION99.5
1.18-1.210.17041290.14922686X-RAY DIFFRACTION99.61
1.21-1.240.15581410.14932642X-RAY DIFFRACTION98.72
1.24-1.280.1651440.15482635X-RAY DIFFRACTION99.82
1.28-1.320.15811300.15392709X-RAY DIFFRACTION99.75
1.32-1.370.15531480.15792675X-RAY DIFFRACTION99.65
1.37-1.420.16421310.15872704X-RAY DIFFRACTION99.86
1.42-1.490.15571320.15742686X-RAY DIFFRACTION99.23
1.49-1.560.1541260.15162704X-RAY DIFFRACTION99.58
1.56-1.660.17791490.15522691X-RAY DIFFRACTION99.89
1.66-1.790.1691640.16752689X-RAY DIFFRACTION99.83
1.79-1.970.17721540.17932707X-RAY DIFFRACTION99.51
1.97-2.260.18691420.17682744X-RAY DIFFRACTION99.62
2.26-2.840.20541570.19792766X-RAY DIFFRACTION99.93
2.84-43.50.1961610.17532895X-RAY DIFFRACTION99.67

+
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