Human ubiquitin in the P1 space group

Experimental Data Snapshot

  • Resolution: 1.32 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

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This is version 1.2 of the entry. See complete history


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 F Struct Biol Commun 72: 29-35

  • DOI: https://doi.org/10.1107/S2053230X15023390
  • Primary Citation of Related Structures:  

  • 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
76Homo sapiensMutation(s): 0 
Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens)
Explore P0CG47 
Go to UniProtKB:  P0CG47
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CG47
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MG

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.32 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 29.961α = 88.52
b = 30.182β = 79.12
c = 41.414γ = 67.37
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
AutoPROCdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Economy and CompetitivenessSpainBIO2012-39922-C02-01/02

Revision History  (Full details and data files)

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