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- PDB-2ogo: The crystal structure of the large ribosomal subunit from Deinoco... -

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Basic information

Entry
Database: PDB / ID: 2ogo
TitleThe crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with the pleuromutilin derivative retapamulin (SB-275833)
Components
  • 23S ribosomal RNA
  • 50S ribosomal protein L3
KeywordsRIBOSOME / retapamulin / SB-275833 / pleuromutilin / PTC / peptidyl transferase center / antibiotic
Function / homology
Function and homology information


cytosolic large ribosomal subunit / rRNA binding / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L3, conserved site / Ribosomal protein L3 signature. / Ribosomal protein L3 / Ribosomal protein L3 / Translation protein, beta-barrel domain superfamily
Similarity search - Domain/homology
Retapamulin / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL3
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.66 Å
AuthorsDavidovich, C. / Bashan, A. / Auerbach-Nevo, T. / Yonath, A.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Induced-fit tightens pleuromutilins binding to ribosomes and remote interactions enable their selectivity.
Authors: Davidovich, C. / Bashan, A. / Auerbach-Nevo, T. / Yaggie, R.D. / Gontarek, R.R. / Yonath, A.
History
DepositionJan 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: 23S ribosomal RNA
B: 50S ribosomal protein L3
0: Retapamulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)956,4003
Polymers955,8822
Non-polymers5181
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)170.115, 405.873, 695.243
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
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)
#2: Protein 50S ribosomal protein L3 / Coordinate model: Cα atoms only


Mass: 22477.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXK2
#3: Chemical ChemComp-G34 / Retapamulin


Mass: 517.763 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H47NO4S / Comment: antibiotic*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 9

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Sample preparation

CrystalDensity Matthews: 6.28 Å3/Da / Density % sol: 80.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Ethanol, Dimethylhexanediol, MgCl2, HEPES, NH4Cl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1Ethanol11
2Dimethylhexanediol11
3MgCl211
4HEPES11
5NH4Cl11
6H2O11
7Ethanol12
8Dimethylhexanediol12
9MgCl212
10HEPES12
11NH4Cl12

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2005
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 3.66→30 Å / Num. obs: 243598 / % possible obs: 93.1 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 9.1
Reflection shellResolution: 3.66→3.79 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.791 / Mean I/σ(I) obs: 1.4 / % possible all: 70

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.66→29.96 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 12688274.59 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: the protein of this entry contains CA only
RfactorNum. reflection% reflectionSelection details
Rfree0.334 12167 5 %RANDOM
Rwork0.26 ---
obs-243559 93 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-14.126 Å20 Å20 Å2
2---49.692 Å20 Å2
3---35.566 Å2
Refinement stepCycle: LAST / Resolution: 3.66→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms205 59336 36 0 59577
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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