6D92

Ternary RsAgo Complex with Guide RNA and Target DNA Containing A-A non-canonical pair at position 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Accommodation of Helical Imperfections in Rhodobacter sphaeroides Argonaute Ternary Complexes with Guide RNA and Target DNA.

Liu, Y.Esyunina, D.Olovnikov, I.Teplova, M.Kulbachinskiy, A.Aravin, A.A.Patel, D.J.

(2018) Cell Rep 24: 453-462


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
A, F
791Rhodobacter sphaeroides (strain ATCC 17025 / ATH 2.4.3)Mutation(s): 0 
Find proteins for A4WYU7 (Rhodobacter sphaeroides (strain ATCC 17025 / ATH 2.4.3))
Go to UniProtKB:  A4WYU7
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(P*UP*UP*AP*CP*UP*GP*CP*AP*CP*AP*GP*GP*UP*GP*AP*CP*GP*A)-3')C,H18Rhodobacter sphaeroides ATCC 17025
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*CP*GP*TP*CP*AP*CP*CP*TP*GP*TP*GP*CP*AP*GP*AP*AP*AP*C)-3')G19Rhodobacter sphaeroides ATCC 17025
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*GP*TP*CP*GP*TP*CP*AP*CP*CP*TP*GP*TP*GP*CP*AP*GP*AP*AP*AP*C)-3')J21Rhodobacter sphaeroides ATCC 17025
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, F
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
C, H
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

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Download CCD File 
H
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 68.237α = 90.00
b = 118.942β = 95.72
c = 118.559γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
PDB_EXTRACTdata extraction
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-07-25
    Type: Initial release