Conserved hypothetical protein from Pyrococcus furiosus Pfu-392566-001

Experimental Data Snapshot

  • Resolution: 1.20 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report

This is version 1.5 of the entry. See complete history


(NZ)CH...O contacts assist crystallization of a ParB-like nuclease.

Shaw, N.Cheng, C.Tempel, W.Chang, J.Ng, J.Wang, X.Y.Perrett, S.Rose, J.Rao, Z.Wang, B.C.Liu, Z.J.

(2007) BMC Struct Biol 7: 46-46

  • DOI: https://doi.org/10.1186/1472-6807-7-46
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The major bottleneck for determination of 3 D structures of proteins using X-rays is the production of diffraction quality crystals. Often proteins are subjected to chemical modification to improve the chances of crystallization Here, we report the successful crystallization of a nuclease employing a reductive methylation protocol. The key to crystallization was the successful introduction of 44 new cohesive (NZ) CH...O contacts (3.2-3.7 A) by the addition of 2 methyl groups to the side chain amine nitrogen (NZ) of 9 lysine residues of the nuclease. The new contacts dramatically altered the crystallization properties of the protein, resulting in crystals that diffracted to 1.2 A resolution. Analytical ultracentrifugation analysis and thermodynamics results revealed a more compact protein structure with better solvent exclusion of buried Trp residues in the folded state of the methylated protein, assisting crystallization. In this study, introduction of novel cohesive (NZ)CH...O contacts by reductive methylation resulted in the crystallization of a protein that had previously resisted crystallization in spite of extensive purification and crystallization space screening. Introduction of (NZ)CH...O contacts could provide a solution to crystallization problems for a broad range of protein targets.

  • Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. neilshaw@moon.ibp.ac.cn

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Conserved hypothetical protein242Pyrococcus furiosusMutation(s): 9 
Find proteins for Q8U3S5 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U3S5 
Go to UniProtKB:  Q8U3S5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8U3S5
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MLY
Experimental Data & Validation

Experimental Data

  • Resolution: 1.20 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.148α = 90
b = 40.099β = 122.29
c = 65.671γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
ARP/wARPmodel building
PDB_EXTRACTdata extraction
MolProbitymodel building

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-10
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2013-01-09
    Changes: Database references
  • Version 1.4: 2017-10-04
    Changes: Refinement description
  • Version 1.5: 2023-12-27
    Changes: Data collection, Database references, Derived calculations