1OID

5'-Nucleotidase (E. coli) with an Engineered Disulfide Bridge (S228C, P513C)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report


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


Literature

Trapping a 96 Degree Domain Rotation in Two Distinct Conformations by Engineered Disulfide Bridges

Schultz-Heienbrok, R., Maier, T., Straeter, N.

(2004) Protein Sci 13: 1811

  • DOI: 10.1110/ps.04629604
  • Primary Citation of Related Structures:  
    1OIE, 1OID, 1OI8

  • PubMed Abstract: 

    • Engineering disulfide bridges is a common technique to lock a protein movement in a defined conformational state. We have designed two double mutants of Escherichia coli 5'-nucleotidase to trap the enzyme in both an open (S228C, P513C) and a closed (P90C, L424C) conformation by the formation of disulfide bridges ...

    Engineering disulfide bridges is a common technique to lock a protein movement in a defined conformational state. We have designed two double mutants of Escherichia coli 5'-nucleotidase to trap the enzyme in both an open (S228C, P513C) and a closed (P90C, L424C) conformation by the formation of disulfide bridges. The mutant proteins have been expressed, purified, and crystallized, to structurally characterize the designed variants. The S228C, P513C is a double mutant crystallized in two different crystal forms with three independent conformers, which differ from each other by a rotation of up to 12 degrees of the C-terminal domain with respect to the N-terminal domain. This finding, as well as an analysis of the domain motion in the crystal, indicates that the enzyme still exhibits considerable residual domain flexibility. In the double mutant that was designed to trap the enzyme in the closed conformation, the structure analysis reveals an unexpected intermediate conformation along the 96 degrees rotation trajectory between the open and closed enzyme forms. A comparison of the five independent conformers analyzed in this study shows that the domain movement of the variant enzymes is characterized by a sliding movement of the residues of the domain interface along the interface, which is in contrast to a classical closure motion where the residues of the domain interface move perpendicular to the interface.

    Related Citations: 
    • E. Coli 5'-Nucleotidase Undergoes a Hinge-Bending Domain Rotation Resembling a Ball-and-Socket Motion
      Knoefel, T., Straeter, N.
      (2001) J Mol Biol 309: 255
    • X-Ray Structure of the Escherichia Coli Periplasmic 5'-Nucleotidase Containing a Dimetal Catalytic Site
      Knoefel, T., Straeter, N.
      (1999) Nat Struct Biol 6: 448
    Organizational Affiliation: 

    Biotechnologisch-Biomedizinisches Zentrum der Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN USHA A, B532Escherichia coliMutation(s): 2 
EC: 3.1.3.5 (PDB Primary Data), 3.6.1.45 (PDB Primary Data)
Find proteins for P07024 (Escherichia coli (strain K12))
Explore P07024 
Go to UniProtKB:  P07024
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI
Download Ideal Coordinates CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.496α = 90
b = 93.708β = 97.71
c = 82.901γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
MOLREPphasing
REFMACrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-06-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance