2O45 | pdb_00002o45

Structure of the 23S rRNA of the large ribosomal subunit from Deinococcus Radiodurans in complex with the macrolide RU-69874

PDB DOI: https://doi.org/10.2210/pdb2O45/pdb
NAKB: 2O45

Classification: RNA
Organism(s): Deinococcus radiodurans
Mutation(s): No

Deposited: 2006-12-03 Released: 2007-12-04
Deposition Author(s): Baram, D., Pyetan, E., Auerbach-Nevo, T., Yonath, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.60 Å
R-Value Free:
0.364 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Chemical Parameters Influencing Fine Tuning in the Binding of Macrolide Antibiotics to the Ribosomal Tunnel

Baram, D., Pyetan, E., Auerbach-Nevo, T., Yonath, A.

To be published.

Macromolecule Content

Total Structure Weight: 934.38 kDa
Atom Count: 59,428
Modeled Residue Count: 2,766
Deposited Residue Count: 2,880
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 1
23S rRNA	A	2,880	Deinococcus radiodurans
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RU6 Query on RU6 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(3AS,4R,7R,8S,9S,10R,11R,13R,15R,15AR)-4-ETHYL-11-METHOXY-3A,7,9,11,13,15-HEXAMETHYL-2,6,14-TRIOXO-1-[4-(4-PYRIDIN-3-YL-1H-IMIDAZOL-1-YL)BUTYL]-10-{[3,4,6-TRIDEOXY-3-(DIMETHYLAMINO)-BETA-D-XYLO-HEXOPYRANOSYL]OXY}TETRADECAHYDRO-2H-OXACYCLOTETRADECINO[4,3-D][1,3]OXAZOL-8-YL 2,6-DIDEOXY-3-C-METHYL-3-O-METHYL-ALPHA-L-RIBO-HEXOPYRANOSIDE C₅₁ H₈₁ N₅ O₁₃ LSUFMKOMGWIEMZ-IBNZHXLDSA-N		Interactions Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.60 Å
R-Value Free: 0.364 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.01	α = 90
b = 411.475	β = 90
c = 697.616	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-12-04

Deposition Author(s):

Auerbach-Nevo, T.

Revision History (Full details and data files)

Version 1.0: 2007-12-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-08-30
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.