Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 16.72 kDa 
• Atom Count: 1489 
• Residue Count: 136 
• Unique protein chains: 1

1EUW

ATOMIC RESOLUTION STRUCTURE OF E. COLI DUTPASE

• DOI: 10.2210/pdb1EUW/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 2000-04-17 Released: 2000-05-03 
• Deposition Author(s): Gonzalez, A., Cedergren, E., Larsson, G., Persson, R.

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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 

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

• PubMed: 11375495 
• 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 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.

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Organizational Affiliation: 

European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22603 Hamburg, Germany. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE	A	152	Escherichia coli	Mutation(s): 0  EC: 3.6.1.23
Find proteins for P06968 (Escherichia coli (strain K12)) Go to UniProtKB:  P06968

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EMC	A	ETHYL MERCURY ION C2 H5 Hg MJOUBOKSWBMNGQ-UHFFFAOYSA-N
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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 = 85.742	α = 90
b = 85.742	β = 90
c = 61.749	γ = 120

Software Package:

Software Name	Purpose
ARP/wARP	model building
SHELXL-97	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-04-17 
• Released Date: 2000-05-03 
Deposition Author(s): Gonzalez, A., Cedergren, E., Larsson, G., Persson, R.

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