4K7W | pdb_00004k7w

Crystal structure of Zn3-hUb(human ubiquitin) adduct from a solution 100 mM zinc acetate/1.3 mM hUb

• PDB DOI: https://doi.org/10.2210/pdb4K7W/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-04-17 Released: 2013-05-08 
• Deposition Author(s): Fermani, S., Falini, G., Calvaresi, M., Bottoni, A., Arnesano, F., Natile, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.267 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

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

• PubMed: 24123543 
• DOI: https://doi.org/10.1002/chem.201302229
• Primary Citation Related Structures: 
  4K7S, 4K7U, 4K7W


• 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 type of selected conformer is shown to determine the crystal packing, which varies from orthorhombic to cubic symmetry.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 26.56 kDa 
• Atom Count: 2,108 
• Modeled Residue Count: 216 
• Deposited Residue Count: 228 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ubiquitin	A, B, C	76	Homo sapiens	Mutation(s): 0  Gene Names: UBC EC: 6.3.2.19
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
PHAROS:  P0CG48 GTEx:  ENSG00000150991

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A], E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], L [auth C], M [auth C], N [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	H [auth A], O [auth C], P [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.267 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.88	α = 90
b = 50.51	β = 90
c = 93.95	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-08 
Deposition Author(s): Fermani, S., Falini, G., Calvaresi, M., Bottoni, A., Arnesano, F., Natile, G.

Revision History  

• Version 1.0: 2013-05-08
  Type: Initial release
  
• Version 1.1: 2017-03-01
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description