3B4A

T. tengcongensis glmS ribozyme with G40A mutation, bound to glucosamine-6-phosphate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.246 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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


Literature

Essential Role of an Active-Site Guanine in glmS Ribozyme Catalysis.

Klein, D.J., Been, M.D., Ferre-D'Amare, A.R.

(2007) J Am Chem Soc 129: 14858-14859

  • DOI: https://doi.org/10.1021/ja0768441
  • Primary Citation of Related Structures:  
    3B4A, 3B4B, 3B4C

  • PubMed Abstract: 

    The glmS ribozyme is a catalytic riboswitch that is activated for endonucleolytic cleavage by the coenzyme glucosamine-6-phosphate. Using kinetic assays and X-ray crystallography, we identify an active-site mutation of a conserved guanine that abolishes catalysis without perturbing coenzyme binding. Our results provide evidence that coenzyme function requires a specific nucleobase to interact with the nucleophile of the cleavage reaction.

    • Organizational Affiliation: 

    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, USA.


Macromolecules
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
glmS ribozyme substrate RNA28Caldanaerobacter subterraneus subsp. tengcongensis
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
glmS ribozyme RNA125Caldanaerobacter subterraneus subsp. tengcongensis
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GLP
Query on GLP
Download Ideal Coordinates CCD File 
C [auth A]2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose
C6 H14 N O8 P
XHMJOUIAFHJHBW-UKFBFLRUSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
D [auth A]
E [auth B]
F [auth B]
G [auth B]
H [auth B]
D [auth A],
E [auth B],
F [auth B],
G [auth B],
H [auth B],
I [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.246 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 177.154α = 90
b = 41.692β = 90
c = 77.699γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Structure summary