1EUW

ATOMIC RESOLUTION STRUCTURE OF E. COLI DUTPASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.141 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Atomic resolution structure of Escherichia coli dUTPase determined ab initio.

Gonzalez, A.Larsson, G.Persson, R.Cedergren-Zeppezauer, E.

(2001) Acta Crystallogr D Biol Crystallogr 57: 767-774

  • DOI: 10.1107/s0907444901004255
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Cryocooled crystals of a mercury complex of Escherichia coli dUTPase diffract to atomic resolution. Data to 1.05 A resolution were collected from a derivative crystal and the structure model was derived from a Fourier map with phases calculated from ...

    Cryocooled crystals of a mercury complex of Escherichia coli dUTPase diffract to atomic resolution. Data to 1.05 A resolution were collected from a derivative crystal and the structure model was derived from a Fourier map with phases calculated from the coordinates of the Hg atom (one site per subunit of the trimeric enzyme) using the program ARP/wARP. After refinement with anisotropic temperature factors a highly accurate model of the bacterial dUTPase was obtained. Data to 1.45 A from a native crystal were also collected and the 100 K structures were compared. Inspection of the refined models reveals that a large part of the dUTPase remains rather mobile upon freezing, with 14% of the main chain being totally disordered and with numerous side chains containing disordered atoms in multiple discrete conformations. A large number of those residues surround the active-site cavity. Two glycerol molecules (the cryosolvent) occupy the deoxyribose-binding site. Comparison between the native enzyme and the mercury complex shows that the active site is not adversely affected by the binding of mercury. An unexpected effect seems to be a stabilization of the crystal lattice by means of long-range interactions, making derivatization a potentially useful tool for further studies of inhibitor-substrate-analogue complexes of this protein at very high resolution.


    Organizational Affiliation

    European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22603 Hamburg, Germany. ana@slac.stanford.edu



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASEA152Escherichia coliMutation(s): 0 
EC: 3.6.1.23
Find proteins for P06968 (Escherichia coli (strain K12))
Explore P06968 
Go to UniProtKB:  P06968
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EMC
Query on EMC

Download CCD File 
A
ETHYL MERCURY ION
C2 H5 Hg
MJOUBOKSWBMNGQ-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.141 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.742α = 90
b = 85.742β = 90
c = 61.749γ = 120
Software Package:
Software NamePurpose
ARP/wARPmodel building
SHELXL-97refinement
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-05-03
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2014-06-04
    Changes: Atomic model
  • Version 1.4: 2017-10-04
    Changes: Refinement description