[English] 日本語
Yorodumi
- PDB-5ifg: Crystal structure of HigA-HigB complex from E. Coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ifg
TitleCrystal structure of HigA-HigB complex from E. Coli
Components
  • Antitoxin HigA
  • mRNA interferase HigB
KeywordsHYDROLASE/ANTITOXIN / mRNA interferase / HYDROLASE-ANTITOXIN complex
Function / homology
Function and homology information


toxin-antitoxin complex / regulation of growth / core promoter sequence-specific DNA binding / regulation of mRNA stability / RNA endonuclease activity / Hydrolases; Acting on ester bonds / negative regulation of translation / regulation of DNA-templated transcription / protein homodimerization activity / RNA binding
Similarity search - Function
Toxin-antitoxin system, mRNA interferase HigB / HigB_toxin, RelE-like toxic component of a toxin-antitoxin system / Antitoxin HigA / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily
Similarity search - Domain/homology
mRNA interferase toxin HigB / Antitoxin HigA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.702 Å
AuthorsYang, J.S. / Zhou, K. / Gao, z.Q. / Liu, Q.S. / Dong, Y.H.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2016
Title: Structural insight into the E. coli HigBA complex
Authors: Yang, J. / Zhou, K. / Liu, P. / Dong, Y. / Gao, Z. / Zhang, J. / Liu, Q.
History
DepositionFeb 26, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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: mRNA interferase HigB
B: Antitoxin HigA
C: mRNA interferase HigB
D: Antitoxin HigA


Theoretical massNumber of molelcules
Total (without water)55,0194
Polymers55,0194
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint-59 kcal/mol
Surface area22730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.924, 77.924, 180.634
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein mRNA interferase HigB / hypothesis mRNA interferase HigB / Endoribonuclease HigB / Toxin HigB


Mass: 12266.822 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: higB, ygjN, b3083, JW3054 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P64578, Hydrolases; Acting on ester bonds
#2: Protein Antitoxin HigA / hypothesis mRNA interferase HigA


Mass: 15242.830 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: higA, ygjM, b3082, JW3053 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P67701
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 61.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: 0.2M (NH4)2SO4, 0.1M Bis-Tris pH5.3, 20%(w/v) PEG3350, 0.01M KCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9792 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.33
ReflectionResolution: 2.7→50 Å / Num. obs: 35954 / % possible obs: 99.2 % / Redundancy: 17.4 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 65.78
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 20.9 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 14.67 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.702→44.928 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.79 / Stereochemistry target values: TWIN_LSQ_F
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS AND I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflectionSelection details
Rfree0.2308 1710 5.14 %random selection
Rwork0.1985 ---
obs0.2019 33261 98.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.702→44.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3408 0 0 0 3408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133479
X-RAY DIFFRACTIONf_angle_d1.6684700
X-RAY DIFFRACTIONf_dihedral_angle_d17.931268
X-RAY DIFFRACTIONf_chiral_restr0.067535
X-RAY DIFFRACTIONf_plane_restr0.006598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7029-2.78240.36911470.3072658X-RAY DIFFRACTION94
2.7824-2.87210.36971370.30372641X-RAY DIFFRACTION95
2.8721-2.97470.28821420.28122613X-RAY DIFFRACTION95
2.9747-3.09370.28481360.26412679X-RAY DIFFRACTION95
3.0937-3.23430.28811650.24492607X-RAY DIFFRACTION94
3.2343-3.40460.22021730.22152650X-RAY DIFFRACTION94
3.4046-3.61760.24871250.21492627X-RAY DIFFRACTION94
3.6176-3.89630.21311190.20372678X-RAY DIFFRACTION95
3.8963-4.28730.18611510.17252637X-RAY DIFFRACTION94
4.2873-4.90520.18721440.14332644X-RAY DIFFRACTION95
4.9052-6.17070.21491450.17072639X-RAY DIFFRACTION95
6.1707-29.4370.22761240.17482433X-RAY DIFFRACTION87

+
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