3DVV | pdb_00003dvv

Crystal structure of HIV-1 subtype F DIS extended duplex RNA bound to ribostamycin (U267OMe)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.277 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.268 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 
    0.268 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A fast strategy for Selenium derivatization and phasing of RNA structures

Olieric, V.Rieder, U.Lang, K.Serganov, A.Schulze-Brise, C.Micura, R.Dumas, P.Ennifar, E.

To be published.

Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
HIV-1 genomic RNA
A, B
23N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RIO
Query on RIO

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B]
RIBOSTAMYCIN
C17 H34 N4 O10
NSKGQURZWSPSBC-VVPCINPTSA-N
K
Query on K

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
G [auth B],
H [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.277 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.268 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 0.268 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.703α = 90
b = 30.489β = 122.25
c = 58.004γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary