3DVV | pdb_00003dvv

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

PDB DOI: https://doi.org/10.2210/pdb3DVV/pdb
NAKB: 3DVV

Classification: RNA
Mutation(s): No

Deposited: 2008-07-21 Released: 2008-08-12
Deposition Author(s): Ennifar, E., Dumas, P., Olieric, V.

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.

Macromolecule Content

Total Structure Weight: 15.9 kDa
Atom Count: 1,091
Modeled Residue Count: 46
Deposited Residue Count: 46
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
HIV-1 genomic RNA	A, B	23	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RIO Query on RIO Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B]	RIBOSTAMYCIN C₁₇ H₃₄ N₄ O₁₀ NSKGQURZWSPSBC-VVPCINPTSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain F [auth A] Focus chain I [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], G [auth B], H [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

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 = 99.703	α = 90
b = 30.489	β = 122.25
c = 58.004	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-08-12

Deposition Author(s):

Ennifar, E.

Dumas, P.

Olieric, V.

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