4PIG

Crystal structure of the ubiquitin K11S mutant

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.952 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Enhancing ubiquitin crystallization through surface-entropy reduction.

Loll, P.J., Xu, P., Schmidt, J.T., Melideo, S.L.

(2014) Acta Crystallogr.,Sect.F 70: 1434-1442

  • DOI: 10.1107/S2053230X14019244
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Ubiquitin has many attributes suitable for a crystallization chaperone, including high stability and ease of expression. However, ubiquitin contains a high surface density of lysine residues and the doctrine of surface-entropy reduction suggests that ...

    Ubiquitin has many attributes suitable for a crystallization chaperone, including high stability and ease of expression. However, ubiquitin contains a high surface density of lysine residues and the doctrine of surface-entropy reduction suggests that these lysines will resist participating in packing interactions and thereby impede crystallization. To assess the contributions of these residues to crystallization behavior, each of the seven lysines of ubiquitin was mutated to serine and the corresponding single-site mutant proteins were expressed and purified. The behavior of these seven mutants was then compared with that of the wild-type protein in a 384-condition crystallization screen. The likelihood of obtaining crystals varied by two orders of magnitude within this set of eight proteins. Some mutants crystallized much more readily than the wild type, while others crystallized less readily. X-ray crystal structures were determined for three readily crystallized variants: K11S, K33S and the K11S/K63S double mutant. These structures revealed that the mutant serine residues can directly promote crystallization by participating in favorable packing interactions; the mutations can also exert permissive effects, wherein crystallization appears to be driven by removal of the lysine rather than by addition of a serine. Presumably, such permissive effects reflect the elimination of steric and electrostatic barriers to crystallization.

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
A, B, C, D
76Homo sapiensMutation(s): 1 
Gene Names: UBA52 (UBCEP2)
Find proteins for P62987 (Homo sapiens)
Go to Gene View: UBA52
Go to UniProtKB:  P62987
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA
Download SDF File 
Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL
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Download CCD File 
A, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA
Download SDF File 
Download CCD File 
A, B, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.952 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 47.700α = 90.00
b = 61.820β = 90.00
c = 91.500γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
CrystalCleardata collection
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM079508

Revision History 

  • Version 1.0: 2014-10-29
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence, Derived calculations, Other, Source and taxonomy