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- PDB-1p9x: THE CRYSTAL STRUCTURE OF THE 50S LARGE RIBOSOMAL SUBUNIT FROM DEI... -

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Basic information

Entry
Database: PDB / ID: 1p9x
TitleTHE CRYSTAL STRUCTURE OF THE 50S LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH TELITHROMYCIN KETOLIDE ANTIBIOTIC
Components23S RIBOSOMAL RNA
KeywordsRIBOSOME / RIBOSOMES / TRNA / KETOLIDE / MACROLIDE / ANTIBIOTIC / EXIT-TUNNEL / BLOCKAGE
Function / homologyTELITHROMYCIN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000)
Function and homology information
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsBerisio, R. / Harms, J. / Schluenzen, F. / Zarivach, R. / Hansen, H.A. / Fucini, P. / Yonath, A.
Citation
Journal: J.Bacteriol. / Year: 2003
Title: Structural insight into the antibiotic action of telithromycin against resistant mutants
Authors: Berisio, R. / Harms, J. / Schluenzen, F. / Zarivach, R. / Hansen, H.A. / Fucini, P. / Yonath, A.
#1: Journal: Nature / Year: 2001
Title: Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Centre in Eubacteria
Authors: Schlunzen, F. / Zarivach, R. / Harms, J. / Bashan, A. / Tocilj, A. / Albrecht, R. / Yonath, A. / Franceschi, F.
History
DepositionMay 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 27, 2021Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / pdbx_validate_chiral / struct_site
Item: _chem_comp.pdbx_synonyms / _struct_site.pdbx_auth_asym_id ..._chem_comp.pdbx_synonyms / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 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
0: 23S RIBOSOMAL RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)934,2172
Polymers933,4051
Non-polymers8121
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)170.000, 414.500, 693.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Cell settingorthorhombic
Space group name H-MI222

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Components

#1: RNA chain 23S RIBOSOMAL RNA


Mass: 933405.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: GenBank: 6460405
#2: Chemical ChemComp-TEL / TELITHROMYCIN / (3aS,4R,7R,9R,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,8,14-tetraoxo-1-{4-[4-(pyridin-3-yl)-1H-imidazol-1-yl]butyl}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-10-yl 3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranoside


Mass: 812.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H65N5O10 / Comment: antibiotic*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 10

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Sample preparation

CrystalDensity Matthews: 4 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 273 K / Method: evaporation / pH: 7 / Details: pH 7., EVAPORATION, temperature 273K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.8 / Method: vapor diffusion / Details: Harms, J., (2001) Cell, 107, 679.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mM1reservoirMgCl2
260 mM1reservoirNH4Cl
35 mM1reservoirKCl
410 mMHEPES1reservoirpH7.8

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONAPS 19-ID11.033
SYNCHROTRONESRF ID14-42
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 15, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI111SINGLE WAVELENGTHMx-ray1
2SI311SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.0331
21
ReflectionResolution: 3.4→20 Å / Num. obs: 273922 / % possible obs: 82.7 % / Observed criterion σ(I): -1 / Redundancy: 3.4 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.181 / Net I/σ(I): 3.4
Reflection shellResolution: 3.4→3.46 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 1.5 / % possible all: 70.1
Reflection
*PLUS
Highest resolution: 3.4 Å / Lowest resolution: 20 Å / Redundancy: 3.4 %
Reflection shell
*PLUS
Highest resolution: 3.4 Å / % possible obs: 70.1 % / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
CNSrefinement
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NKW

1nkw


Resolution: 3.4→15 Å / Rfactor Rfree error: 0.003 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.34 9254 5 %RANDOM
Rwork0.273 ---
all0.291 273922 --
obs0.28 245223 --
Refine analyze
FreeObs
Luzzati coordinate error0.05 Å0.04 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 3.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 58759 58 0 58817
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.7
Refinement
*PLUS
Highest resolution: 3.4 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.34 / Rfactor Rwork: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS

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