4HEI

2A X-RAY STRUCTURE OF HPF from VIBRIO CHOLERAE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.262 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structure of Vibrio cholerae ribosome hibernation promoting factor.

De Bari, H.Berry, E.A.

(2013) Acta Crystallogr.,Sect.F 69: 228-236

  • DOI: 10.1107/S1744309113000961

  • PubMed Abstract: 
  • The X-ray crystal structure of ribosome hibernation promoting factor (HPF) from Vibrio cholerae is presented at 2.0 Å resolution. The crystal was phased by two-wavelength MAD using cocrystallized cobalt. The asymmetric unit contained two molecules of ...

    The X-ray crystal structure of ribosome hibernation promoting factor (HPF) from Vibrio cholerae is presented at 2.0 Å resolution. The crystal was phased by two-wavelength MAD using cocrystallized cobalt. The asymmetric unit contained two molecules of HPF linked by four Co atoms. The metal-binding sites observed in the crystal are probably not related to biological function. The structure of HPF has a typical β-α-β-β-β-α fold consistent with previous structures of YfiA and HPF from Escherichia coli. Comparison of the new structure with that of HPF from E. coli bound to the Thermus thermophilus ribosome [Polikanov et al. (2012), Science, 336, 915-918] shows that no significant structural changes are induced in HPF by binding.


    Organizational Affiliation

    Biochemistry and Molecular Biology, SUNY Upstate Medical University, 750 E. Adams Avenue, Syracuse, NY 13210, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBOSOME HIBERNATION PROTEIN YHBH
A, B
95Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)Mutation(s): 0 
Find proteins for H9L4N9 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Go to UniProtKB:  H9L4N9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SCN
Query on SCN

Download SDF File 
Download CCD File 
A, B
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
3CO
Query on 3CO

Download SDF File 
Download CCD File 
A, B
COBALT (III) ION
Co
JAWGVVJVYSANRY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.262 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 46.354α = 90.00
b = 46.354β = 90.00
c = 174.492γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
HKL-2000data collection
PHENIXphasing
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-10-03 
  • Released Date: 2012-10-24 
  • Deposition Author(s): De Bari, H., Berry, E.A.
  • This entry supersedes: 4FYL

Revision History 

  • Version 1.0: 2012-10-24
    Type: Initial release
  • Version 1.1: 2012-12-12
    Type: Derived calculations
  • Version 1.2: 2013-03-06
    Type: Database references, Derived calculations, Other
  • Version 1.3: 2013-05-22
    Type: Database references
  • Version 1.4: 2017-06-21
    Type: Database references, Source and taxonomy