[English] 日本語
Yorodumi
- PDB-5yrz: Toxin-Antitoxin complex from Streptococcus pneumoniae -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yrz
TitleToxin-Antitoxin complex from Streptococcus pneumoniae
Components
  • HicA
  • HicB
KeywordsANTITOXIN/HYDROLASE / Toxin / antitoxin / hydrolase / DNA / ANTITOXIN-HYDROLASE complex
Function / homology
Function and homology information


endonuclease activity / mRNA binding
Similarity search - Function
Hypothetical protein. / HicA mRNA interferase family / HicA superfamily / HicA toxin of bacterial toxin-antitoxin, / HicB_like antitoxin of bacterial toxin-antitoxin system / TTHA1013/TTHA0281-like / Metal Transport, Frataxin; Chain A / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.304 Å
AuthorsKang, S.M. / Kim, D.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation of Korea2015R1A2A1A05001894 Korea, Republic Of
National Research Foundation of Korea2014K1A3A1A19067618 Korea, Republic Of
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Functional insights into the Streptococcus pneumoniae HicBA toxin-antitoxin system based on a structural study.
Authors: Kim, D.H. / Kang, S.M. / Park, S.J. / Jin, C. / Yoon, H.J. / Lee, B.J.
History
DepositionNov 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 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: HicB
B: HicA
C: HicB
D: HicA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9858
Polymers53,6044
Non-polymers3804
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-57 kcal/mol
Surface area23280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.263, 116.541, 42.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein HicB


Mass: 16938.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria)
Strain: ATCC BAA-334 / TIGR4 / Gene: SP_1786 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2URC7
#2: Protein HicA


Mass: 9863.560 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria)
Strain: ATCC BAA-334 / TIGR4 / Gene: SP_1787 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2URA5
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.21 Å3/Da / Density % sol: 49.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.5 / Details: 0.1 M Tris, pH 8.5, 2.0 M Ammonium sulfate

-
Data collection

DiffractionMean temperature: 77.2 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 24090 / % possible obs: 99.7 % / Redundancy: 9.9 % / Net I/σ(I): 30.2
Reflection shellResolution: 2.3→2.34 Å

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.304→32.669 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.61
RfactorNum. reflection% reflection
Rfree0.2361 1228 5.11 %
Rwork0.2045 --
obs0.2061 24045 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.304→32.669 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3248 0 21 85 3354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053331
X-RAY DIFFRACTIONf_angle_d0.9634497
X-RAY DIFFRACTIONf_dihedral_angle_d15.8091236
X-RAY DIFFRACTIONf_chiral_restr0.038494
X-RAY DIFFRACTIONf_plane_restr0.004572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3041-2.39630.33791180.25032434X-RAY DIFFRACTION97
2.3963-2.50530.29971350.23972512X-RAY DIFFRACTION100
2.5053-2.63730.26761360.24822503X-RAY DIFFRACTION100
2.6373-2.80250.30231470.24792473X-RAY DIFFRACTION100
2.8025-3.01870.27841510.24662521X-RAY DIFFRACTION100
3.0187-3.32220.26841460.22612518X-RAY DIFFRACTION100
3.3222-3.80240.21331340.19472550X-RAY DIFFRACTION100
3.8024-4.78820.18851250.16382587X-RAY DIFFRACTION100
4.7882-32.67250.19131360.18172719X-RAY DIFFRACTION100

+
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