5D5L | pdb_00005d5l

PreQ1-II riboswitch with an engineered G-U wobble pair bound to Cs+

  • Classification: RNA
  • Organism(s): Lacticaseibacillus rhamnosus LOCK908
  • Mutation(s): No 

  • Deposited: 2015-08-10 Released: 2016-08-10 
  • Deposition Author(s): Wedekind, J.E., Liberman, J.A., Salim, M.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Center for Research Resources (NIH/NCRR)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.247 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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


Literature

Cesium(I) binding to G-U-wobble base pairs in preQ1 riboswitches with implications for crystallographic phasing

Belashov, I.A., Liberman, J.A., Salim, M., Wedekind, J.E.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
PreQ1-II riboswitch
A, B, C, D
77Lacticaseibacillus rhamnosus LOCK908
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PRF
Query on PRF
Download Ideal Coordinates CCD File 
JA [auth B],
QA [auth C],
U [auth A],
ZA [auth D]		7-DEAZA-7-AMINOMETHYL-GUANINE
C7 H9 N5 O
MEYMBLGOKYDGLZ-UHFFFAOYSA-N
CS
Query on CS
Download Ideal Coordinates CCD File 
BA [auth B]
CA [auth B]
DA [auth B]
E [auth A]
EA [auth B]
BA [auth B],
CA [auth B],
DA [auth B],
E [auth A],
EA [auth B],
F [auth A],
FA [auth B],
G [auth A],
GA [auth B],
H [auth A],
HA [auth B],
I [auth A],
IA [auth B],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
NA [auth C],
O [auth A],
OA [auth C],
P [auth A],
PA [auth C],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
UA [auth D],
VA [auth D],
WA [auth D],
XA [auth D],
YA [auth D]
CESIUM ION
Cs
NCMHKCKGHRPLCM-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth D]
BB [auth D]
CB [auth D]
KA [auth B]
AA [auth A],
AB [auth D],
BB [auth D],
CB [auth D],
KA [auth B],
LA [auth B],
MA [auth B],
RA [auth C],
SA [auth C],
TA [auth C],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.247 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.358α = 90
b = 57.833β = 107.64
c = 99.493γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
HKL-2000data reduction
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM063162
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesRR026501

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Author supporting evidence, Derived calculations
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description