R1EN(5-227)-ubiquitin fusion

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Crystal Structure Determination of Ubiquitin by Fusion to a Protein That Forms a Highly Porous Crystal Lattice

Maita, N.

(2018) J Am Chem Soc 140: 13546-13549

  • DOI: https://doi.org/10.1021/jacs.8b07512
  • Primary Citation of Related Structures:  
    6A42, 6A43, 6A44

  • PubMed Abstract: 

    The protein crystallization process requires screening of a large number of conditions using a large quantity of high-purity protein, which makes crystal structure analysis difficult. Thus, the development of easy and versatile protein crystallization techniques is both extremely desirable and highly challenging. Here I demonstrate the crystallization and structure determination of ubiquitin by genetic fusion to the highly porous honeycomb lattice of R1EN. I successfully crystallized and collected X-ray data from three R1EN-ubiquitin constructs with various linker lengths under the same conditions as the original R1EN. The crystals diffracted to 1.7-2.4 Å resolution, and the ubiquitin structures were determined with results almost identical to the previously published structure. Moreover, the ubiquitin structure could be solved by molecular replacement using R1EN alone. This method may reduce the effort required for crystallization screening and is applicable to de novo protein structure determination.

  • Organizational Affiliation

    Division of Disease Proteomics, Institute of Advanced Medical Sciences , Tokushima University , 3-18-15 Kuramoto-cho , Tokushima 770-8503 , Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-directed DNA polymerase homolog (R1),Polyubiquitin-C302Bombyx moriHomo sapiens
This entity is chimeric
Mutation(s): 2 
UniProt & NIH Common Fund Data Resources
Find proteins for Q7M4J4 (Bombyx mori)
Explore Q7M4J4 
Go to UniProtKB:  Q7M4J4
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
GTEx:  ENSG00000150991 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ7M4J4P0CG48
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ACY

Download Ideal Coordinates CCD File 
C2 H4 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.193 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.801α = 90
b = 141.801β = 90
c = 38.15γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2018-10-24 
  • Deposition Author(s): Maita, N.

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan15K13747

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2018-11-07
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description