3W5W

Mn2+-GMP complex of nanoRNase (Nrn) from Bacteroides fragilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.215 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the ligand-binding form of nanoRNase from Bacteroides fragilis, a member of the DHH/DHHA1 phosphoesterase family of proteins.

Uemura, Y.Nakagawa, N.Wakamatsu, T.Kim, K.Montelione, G.T.Hunt, J.F.Kuramitsu, S.Masui, R.

(2013) FEBS Lett 587: 2669-2674

  • DOI: https://doi.org/10.1016/j.febslet.2013.06.053
  • Primary Citation of Related Structures:  
    3W5W

  • PubMed Abstract: 

    NanoRNase (Nrn) specifically degrades nucleoside 3',5'-bisphosphate and the very short RNA, nanoRNA, during the final step of mRNA degradation. The crystal structure of Nrn in complex with a reaction product GMP was determined. The overall structure consists of two domains that are interconnected by a flexible loop and form a cleft. Two Mn²⁺ ions are coordinated by conserved residues in the DHH motif of the N-terminal domain. GMP binds near the DHHA1 motif region in the C-terminal domain. Our structure enables us to predict the substrate-bound form of Nrn as well as other DHH/DHHA1 phosphoesterase family proteins.


  • Organizational Affiliation

    Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative exopolyphosphatase-related protein351Bacteroides fragilis YCH46Mutation(s): 0 
Gene Names: BF3900
UniProt
Find proteins for Q64PD9 (Bacteroides fragilis (strain YCH46))
Explore Q64PD9 
Go to UniProtKB:  Q64PD9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ64PD9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.215 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.828α = 90
b = 90.828β = 90
c = 107.878γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-10
    Type: Initial release
  • Version 1.1: 2022-08-24
    Changes: Database references, Derived calculations
  • Version 1.2: 2023-11-08
    Changes: Data collection, Refinement description