4HVY

A thermostable variant of human NUDT18 NUDIX domain obtained by Hot Colony Filtration


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Engineering protein thermostability using a generic activity-independent biophysical screen inside the cell.

Asial, I.Cheng, Y.X.Engman, H.Dollhopf, M.Wu, B.Nordlund, P.Cornvik, T.

(2013) Nat Commun 4: 2901-2901

  • DOI: 10.1038/ncomms3901

  • PubMed Abstract: 
  • Protein stability is often a limiting factor in the development of commercial proteins and biopharmaceuticals, as well as for biochemical and structural studies. Unfortunately, identifying stabilizing mutations is not trivial since most are neutral o ...

    Protein stability is often a limiting factor in the development of commercial proteins and biopharmaceuticals, as well as for biochemical and structural studies. Unfortunately, identifying stabilizing mutations is not trivial since most are neutral or deleterious. Here we describe a high-throughput colony-based stability screen, which is a direct and biophysical read-out of intrinsic protein stability in contrast to traditional indirect activity-based methods. By combining the method with a random mutagenesis procedure, we successfully identify thermostable variants from 10 diverse and challenging proteins, including several biotechnologically important proteins such as a single-chain antibody, a commercial enzyme and an FDA-approved protein drug. We also show that thermostabilization of a protein drug using our approach translates into dramatic improvements in long-term stability. As the method is generic and activity independent, it can easily be applied to a wide range of proteins.


    Organizational Affiliation

    School of Biological Sciences, Nanyang Technological University, 639798 Singapore, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nucleoside diphosphate-linked moiety X motif 18
A
162Homo sapiensMutation(s): 2 
Gene Names: NUDT18 (MTH3)
EC: 3.6.1.58
Find proteins for Q6ZVK8 (Homo sapiens)
Go to Gene View: NUDT18
Go to UniProtKB:  Q6ZVK8
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.166 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 90.200α = 90.00
b = 90.200β = 90.00
c = 75.030γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
MOSFLMdata reduction
PHASERphasing
PHENIXrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-01
    Type: Initial release