6DME

ppGpp Riboswitch bound to ppGpp, thallium acetate structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.702 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

ykkC riboswitches employ an add-on helix to adjust specificity for polyanionic ligands.

Peselis, A.Serganov, A.

(2018) Nat. Chem. Biol. 14: 887-894


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
ppGpp RiboswitchA102Sulfobacillus acidophilus DSM 10332
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
TL
Query on TL

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Download CCD File 
A
THALLIUM (I) ION
Tl
ZLUSCZLCHQSJRU-UHFFFAOYSA-N
 Ligand Interaction
G4P
Query on G4P

Download SDF File 
Download CCD File 
A
GUANOSINE-5',3'-TETRAPHOSPHATE
C10 H17 N5 O17 P4
BUFLLCUFNHESEH-UUOKFMHZSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CCC
Query on CCC
A
RNA LINKINGC9 H13 N3 O10 P2C
GTP
Query on GTP
A
NON-POLYMERC10 H16 N5 O14 P3G
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.702 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 100.184α = 90.00
b = 51.816β = 128.10
c = 77.862γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM112940
National Institutes of Health/National Institute of General Medical SciencesUnited StatesF31GM119357
National Institutes of Health/National Institute of General Medical SciencesUnited StatesT32GM88118

Revision History 

  • Version 1.0: 2018-11-14
    Type: Initial release