3G5I

Crystal Structure of the E.coli RihA pyrimidine nucleosidase bound to a iminoribitol-based inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

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This is version 1.3 of the entry. See complete history. 


Literature

Active site plasticity revealed from the structure of the enterobacterial N-ribohydrolase RihA bound to a competitive inhibitor.

Garau, G., Muzzolini, L., Tornaghi, P., Degano, M.

(2010) BMC Struct Biol 10: 14-14

  • DOI: https://doi.org/10.1186/1472-6807-10-14
  • Primary Citation of Related Structures:  
    3G5I

  • PubMed Abstract: 

    Pyrimidine-preferring N-ribohydrolases (CU-NHs) are a class of Ca2+-dependent enzymes that catalyze the hydrolytic cleavage of the N-glycosidic bond in pyrimidine nucleosides. With the exception of few selected organisms, their physiological relevance in prokaryotes and eukaryotes is yet under investigation.

    • Organizational Affiliation: 

    Biocrystallography Unit, Division of Immunology, Transplantation, and Infectious Diseases - Scientific Institute S. Raffaele, via Olgettina 58, 20132 Milan - Italy.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyrimidine-specific ribonucleoside hydrolase rihA
A, B, C, D
312Escherichia coli K-12Mutation(s): 0 
Gene Names: ybeK
EC: 3.2.2.8
UniProt
Find proteins for P41409 (Escherichia coli (strain K12))
Explore P41409 
Go to UniProtKB:  P41409
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41409
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DNB
Query on DNB
Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
K [auth C],
M [auth D]		(2S,3S,4R,5R)-2-(3,4-diaminophenyl)-5-(hydroxymethyl)pyrrolidine-3,4-diol
C11 H17 N3 O3
YAYMFJWCRXEXGZ-YTWAJWBKSA-N
BME
Query on BME
Download Ideal Coordinates CCD File 
E [auth A]BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.35α = 90
b = 82.91β = 112.15
c = 93.87γ = 90
Software Package:
Software NamePurpose
DNAdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2021-02-17
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Refinement description