[English] 日本語
Yorodumi
- PDB-4p7d: Antitoxin HicB3 crystal structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4p7d
TitleAntitoxin HicB3 crystal structure
ComponentsAntitoxin HicB3
KeywordsTOXIN / toxin-antitoxin complex / homotetramer
Function / homology
Function and homology information


sequence-specific DNA binding / regulation of DNA-templated transcription
Similarity search - Function
Double Stranded RNA Binding Domain - #250 / HicB-like antitoxin of toxin-antitoxin system / HicB_like antitoxin of bacterial toxin-antitoxin system / TTHA1013/TTHA0281-like / Arc-type ribbon-helix-helix / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.781 Å
AuthorsLi de la Sierra-Gallay, I. / Bibi-Triki, S. / van Tilbeurgh, H. / Lazar, N. / Pradel, E.
CitationJournal: J.Bacteriol. / Year: 2014
Title: Functional and Structural Analysis of HicA3-HicB3, a Novel Toxin-Antitoxin System of Yersinia pestis.
Authors: Bibi-Triki, S. / Li de la Sierra-Gallay, I. / Lazar, N. / Leroy, A. / Van Tilbeurgh, H. / Sebbane, F. / Pradel, E.
History
DepositionMar 27, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Other
Revision 1.3Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Antitoxin HicB3
B: Antitoxin HicB3
C: Antitoxin HicB3
D: Antitoxin HicB3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9726
Polymers65,9014
Non-polymers712
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13160 Å2
ΔGint-121 kcal/mol
Surface area26280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.840, 76.870, 118.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Antitoxin HicB3


Mass: 16475.211 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: YPO3369 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0WBS6, UniProt: A0A5P8YCM0*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: polyethylene glycol 3000, MES pH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97911 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.78→46.85 Å / Num. obs: 16491 / % possible obs: 99.5 % / Redundancy: 7.1 % / Biso Wilson estimate: 69.76 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 14.45
Reflection shellResolution: 2.78→2.95 Å / Redundancy: 7 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 2.84 / % possible all: 97.2

-
Processing

Software
NameVersionClassification
XDSdata reduction
SHELXphasing
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.781→46.846 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2824 824 5 %
Rwork0.2051 --
obs0.209 16478 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.42 Å2
Refinement stepCycle: LAST / Resolution: 2.781→46.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4333 0 2 0 4335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114445
X-RAY DIFFRACTIONf_angle_d1.4316002
X-RAY DIFFRACTIONf_dihedral_angle_d15.021654
X-RAY DIFFRACTIONf_chiral_restr0.056633
X-RAY DIFFRACTIONf_plane_restr0.007792
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7814-2.95570.35481330.25672513X-RAY DIFFRACTION97
2.9557-3.18380.31941350.24272573X-RAY DIFFRACTION100
3.1838-3.50410.31951350.22652590X-RAY DIFFRACTION100
3.5041-4.0110.32941370.21272599X-RAY DIFFRACTION100
4.011-5.05240.26661380.18412629X-RAY DIFFRACTION100
5.0524-46.850.23561460.19282750X-RAY DIFFRACTION99

+
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