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5'-NUCLEOTIDASE FROM E. COLI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

X-ray structure of the Escherichia coli periplasmic 5'-nucleotidase containing a dimetal catalytic site.

Knofel, T.Strater, N.

(1999) Nat.Struct.Mol.Biol. 6: 448-453

  • DOI: 10.1038/8253
  • Primary Citation of Related Structures:  
  • Also Cited By: 1OIE, 1OID, 1OI8

  • PubMed Abstract: 
  • The crystal structure of 5'-nucleotidase (5'-NT) from E. coli, also known as UDP-sugar hydrolase, has been determined at 1.7 A resolution. Two zinc ions are present in the active site, which is located in a cleft between two domains. The dimetal cent ...

    The crystal structure of 5'-nucleotidase (5'-NT) from E. coli, also known as UDP-sugar hydrolase, has been determined at 1.7 A resolution. Two zinc ions are present in the active site, which is located in a cleft between two domains. The dimetal center and a catalytic Asp-His dyad are the main players in the catalytic mechanism. Structure-based sequence comparisons show that the structure also provides a model for animal 5'-NTs, which together with other ectonucleotidases terminate the action of nucleotides as extracellular signaling substances in the nervous system.


    Organizational Affiliation

    Institut für Kristallographie, Abteilung Saenger, Freie Universität Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5'-NUCLEOTIDASE
A
550Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: ushA
Find proteins for P07024 (Escherichia coli (strain K12))
Go to UniProtKB:  P07024
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CO3
Query on CO3

Download SDF File 
Download CCD File 
A
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.180 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 83.610α = 90.00
b = 83.610β = 90.00
c = 181.630γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-06-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model