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

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Basic information

Entry
Database: PDB / ID: 1ond
TitleTHE CRYSTAL STRUCTURE OF THE 50S LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH TROLEANDOMYCIN MACROLIDE ANTIBIOTIC
Components
  • 23S RIBOSOMAL RNA
  • 50S ribosomal protein L22
  • 50S ribosomal protein L32
KeywordsRIBOSOME / RIBOSOMES / TRNA / MACROLIDE / ANTIBIOTIC / EXIT-TUNNEL L22 / BLOCKAGE
Function / homology
Function and homology information


large ribosomal subunit / cytosolic large ribosomal subunit / rRNA binding / structural constituent of ribosome / translation / metal ion binding
Similarity search - Function
Ribosomal protein L32p, bacterial type / Ribosomal protein L22, bacterial/chloroplast-type / : / Ribosomal L32p protein family / Ribosomal protein L32p / Ribosomal protein L22/L17, conserved site / Ribosomal protein L22 signature. / Ribosomal protein L22/L17 / Ribosomal protein L22/L17 superfamily / Ribosomal protein L22p/L17e / Zinc-binding ribosomal protein
Similarity search - Domain/homology
TROLEANDOMYCIN / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein uL22
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsBerisio, R. / Schluenzen, F. / Harms, J. / Bashan, A. / Auerbach, T. / Baram, D. / Yonath, A.
Citation
Journal: Nat.Struct.Biol. / Year: 2003
Title: Structural insight into the role of the ribosomal tunnel in cellular regulation
Authors: Berisio, R. / Schluenzen, F. / Harms, J. / Bashan, A. / Auerbach, T. / Baram, D. / 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
DepositionFeb 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
0: 23S RIBOSOMAL RNA
Q: 50S ribosomal protein L22
Z: 50S ribosomal protein L32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)956,2204
Polymers955,4063
Non-polymers8141
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)170.250, 411.090, 695.340
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 L22 / / Coordinate model: Cα atoms only


Mass: 15190.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXJ7
#3: Protein 50S ribosomal protein L32 / / Coordinate model: Cα atoms only


Mass: 6810.017 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: P49228
#4: Chemical ChemComp-TAO / TROLEANDOMYCIN / (3R,5S,6S,7R,8S,11S,12R,13S,14R,15S)-12-[(4-O-ACETYL-2,6-DIDEOXY-3-O-METHYL-ALPHA-L-ARABINO-HEXOPYRANOSYL)OXY]-14-{[2-O-ACETYL-3,4,6-TRIDEOXY-3-(DIMETHYLAMINO)-BETA-D-XYLO-HEXOPYRANOSYL]OXY}-5,7,8,11,13,15-HEXAMETHYL-4,10-DIOXO-1,9-DIOXASPIRO[2.13]HEXADEC-6-YL ACETATE / Troleandomycin


Mass: 813.968 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H67NO15 / Comment: inhibitor*YM
Compound detailsTHE ENTRY CONTAINS ONLY A PART OF THE CRYSTAL ASYMMETRIC UNIT.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4 Å3/Da / Density % sol: 64 %
Crystal growMethod: evaporation / Details: EVAPORATION
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.8 / Method: vapor diffusion
Details: Harms, J.M., (2001) Cell (Cambridge,Mass.), 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 (Å)
SYNCHROTRONAPS 19-ID11.033
SYNCHROTRONESRF ID2921.038
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 15, 2002
RadiationMonochromator: SI111 OR SI311 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0331
21.0381
ReflectionResolution: 3.4→20 Å / Num. all: 291247 / Num. obs: 291247 / % possible obs: 88.1 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 2.4 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 5.4
Reflection shellResolution: 3.4→3.46 Å / Redundancy: 2 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 1.4 / Num. unique all: 13839 / % possible all: 84.5
Reflection
*PLUS
Highest resolution: 3.4 Å / Lowest resolution: 20 Å
Reflection shell
*PLUS
% possible obs: 84.5 %

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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→8 Å / Rfactor Rfree error: 0.003 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER / Details: The protein chains contain CA only.
RfactorNum. reflection% reflectionSelection details
Rfree0.31 10833 5 %RANDOM
Rwork0.261 ---
all0.316 252304 --
obs0.262 217346 --
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→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms188 59336 57 0 59581
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.31
LS refinement shellResolution: 3.4→8 Å
Refinement
*PLUS
Highest resolution: 3.4 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.31 / Rfactor Rwork: 0.262
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.0073

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