Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17354.06 
• Atom Count: 1171 
• Residue Count: 152 
• Unique protein chains: 1

5DK8

Human ubiquitin in the P1 space group

• DOI: 10.2210/pdb5DK8/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2015-09-03 Released: 2015-12-16 
• Deposition Author(s): Camara-Artigas, A., Bacarizo, J.
• Funding Organization(s): Ministry of Economy and Competitiveness 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free: 0.201 
• R-Value Work: 0.178 

Literature

New crystal form of human ubiquitin in the presence of magnesium.

Camara-Artigas, A., Plaza-Garrido, M., Martinez-Rodriguez, S., Bacarizo, J.

(2016) Acta Crystallogr.,Sect.F 72: 29-35

• PubMed: 26750481 
• DOI: 10.1107/S2053230X15023390


• PubMed Abstract: 
  

Ubiquitin is a small globular protein that has a considerable number of lysine residues on its surface. This results in a high surface entropy that precludes the formation of crystal-packing interactions. To date, only a few structures of the native form of ubiquitin have been solved, and most of the crystals that led to these structures were obtained in the presence of different divalent metal cations. In this work, a new crystallographic structure of human ubiquitin solved from crystals grown in the presence of magnesium is presented. The crystals belonged to a triclinic space group, with unit-cell parameters a = 29.96, b = 30.18, c = 41.41 Å, α = 88.52, β = 79.12, γ = 67.37°. The crystal lattice is composed of stacked layers of human ubiquitin molecules with a large hydrophobic interface and a smaller polar interface in which the magnesium ion lies at the junction between adjacent layers in the crystal. The metal ion appears in a hexa-aquo coordination, which is key to facilitating the crystallization of the protein.

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Organizational Affiliation: 

Department of Chemistry and Physics, University of Almeria, Agrifood Campus of International Excellence (ceiA3), Carretera de Sacramento (s/n), 04120 Almeria, Spain.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Polyubiquitin-B	A, B	76	Homo sapiens	Mutation(s): 0  Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens) Go to Gene View: UBB Go to UniProtKB:  P0CG47

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free: 0.201 
• R-Value Work: 0.178 
• Space Group: P 1

Unit Cell:

Length (Å)	Angle (°)
a = 29.961	α = 88.52
b = 30.182	β = 79.12
c = 41.414	γ = 67.37

Software Package:

Software Name	Purpose
AutoPROC	data reduction
PHASER	phasing
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-09-03 
• Released Date: 2015-12-16 
• Deposition Author(s): Camara-Artigas, A., Bacarizo, J.

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Funding Organization	Location	Grant Number
Ministry of Economy and Competitiveness	Spain	BIO2012-39922-C02-01/02

Revision History 

• Version 1.0: 2015-12-16
  Type: Initial release
• Version 1.1: 2016-01-13
  Type: Database references
• Version 1.2: 2016-01-20
  Type: Database references