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- PDB-2o45: Structure of the 23S rRNA of the large ribosomal subunit from Dei... -

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Basic information

Entry
Database: PDB / ID: 2o45
TitleStructure of the 23S rRNA of the large ribosomal subunit from Deinococcus Radiodurans in complex with the macrolide RU-69874
Components23S rRNA
KeywordsRNA / Ribosome / macrolides / tunnel
Function / homologyChem-RU6 / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000)
Function and homology information
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsBaram, D. / Pyetan, E. / Auerbach-Nevo, T. / Yonath, A.
CitationJournal: TO BE PUBLISHED
Title: Chemical Parameters Influencing Fine Tuning in the Binding of Macrolide Antibiotics to the Ribosomal Tunnel
Authors: Baram, D. / Pyetan, E. / Auerbach-Nevo, T. / Yonath, A.
History
DepositionDec 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 23S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)934,3772
Polymers933,4051
Non-polymers9721
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)170.010, 411.475, 697.616
Angle α, β, γ (deg.)90, 90, 90
Int Tables number23
Space group name H-MI222
DetailsThe large ribosomal subunit of Deinococcus radiodurans and Ru-69874

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Components

#1: RNA chain 23S rRNA


Mass: 933405.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant)
#2: Chemical ChemComp-RU6 / (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 / (1R,2R,4R,6R,7R,8S,9S,10R,13R,14S)-7-[(2S,3R,4S,6R)-4-DIMETHYLAMINO-3-HYDROXY-6-METHYL-OXAN-2-YL]OXY-13-ETHYL-9-[(2R,4R,5S,6S)-5-HYDROXY-4-METHOXY-4,6-DIMETHYL-OXAN-2-YL]OXY-6-METHOXY-2,4,6,8,10,14-HEXAMETHYL-17-[4-(4-PYRIDIN-3-YLIMIDAZOL-1-YL)BUTYL]-12,15-DIOXA-17-AZABICYCLO[12.3.0]HEPTADECANE-3,11,16-TRIONE


Mass: 972.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H81N5O13

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 6.54 Å3/Da / Density % sol: 81.18 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONAPS 19-ID1
SYNCHROTRONESRF ID292
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.6→30 Å / Num. obs: 226136 / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Rmerge(I) obs: 0.177

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Processing

SoftwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry - 1nkw

1nkw


Resolution: 3.6→8 Å / σ(F): 1.5 / σ(I): 2 /
RfactorNum. reflection
Rfree0.3644 -
all0.283 -
obs-226136
Refinement stepCycle: LAST / Resolution: 3.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 59359 69 0 59428

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