4K7U

Crystal structure of Zn2.3-hUb (human ubiquitin) adduct from a solution 70 mM zinc acetate/1.3 mM hUb


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Conformational selection of ubiquitin quaternary structures driven by zinc ions.

Fermani, S.Falini, G.Calvaresi, M.Bottoni, A.Calo, V.Mangini, V.Arnesano, F.Natile, G.

(2013) Chemistry 19: 15480-15484

  • DOI: 10.1002/chem.201302229
  • Primary Citation of Related Structures:  
  • Also Cited By: 5NMC, 5NLJ, 5NLI, 5NLF, 5NL5, 5NL4

  • PubMed Abstract: 
  • Zinc ions bridging two ubiquitin molecules (with His68 at the interface) contribute to select a subset of conformers from the noncovalent dimer ensemble, thus restricting quaternary structure dynamics, which hampers apo-protein crystallization. The t ...

    Zinc ions bridging two ubiquitin molecules (with His68 at the interface) contribute to select a subset of conformers from the noncovalent dimer ensemble, thus restricting quaternary structure dynamics, which hampers apo-protein crystallization. The type of selected conformer is shown to determine the crystal packing, which varies from orthorhombic to cubic symmetry.


    Related Citations: 
    • Structural probing of Zn(II), Cd(II) and Hg(II) binding to human ubiquitin.
      Falini, G.,Fermani, S.,Tosi, G.,Arnesano, F.,Natile, G.
      (2008) Chem.Commun.(Camb.) 45: 5960
    • Crystallographic analysis of metal-ion binding to human ubiquitin.
      Arnesano, F.,Belviso, B.D.,Caliandro, R.,Falini, G.,Fermani, S.,Natile, G.,Siliqi, D.
      (2011) Chemistry 17: 1569


    Organizational Affiliation

    Department of Chemistry "G. Ciamician", University of Bologna via F. Selmi 2, 40126 Bologna (Italy).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ubiquitin
A, B, C
76Homo sapiensMutation(s): 0 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Go to Gene View: UBC
Go to UniProtKB:  P0CG48
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B, C
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.161 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.820α = 90.00
b = 50.390β = 90.00
c = 93.620γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-08
    Type: Initial release
  • Version 1.1: 2017-03-01
    Type: Database references