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- PDB-1njo: The crystal structure of the 50S Large ribosomal subunit from Dei... -

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Basic information

Entry
Database: PDB / ID: 1njo
TitleThe crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with a short substrate analog ACCPuromycin (ACCP)
Components
  • 23S ribosomal RNA
  • RNA ACC(Puromycin)
KeywordsRIBOSOME / Ribosomes / tRNA / puromycin / sparsomycin / peptidyl-transferase / peptide bond formation
Function / homology: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000)
Function and homology information
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER MAPS / Resolution: 3.7 Å
AuthorsBashan, A. / Agmon, I. / Zarivatch, R. / Schluenzen, F. / Harms, J.M. / Berisio, R. / Bartels, H. / Hansen, H.A. / Yonath, A.
CitationJournal: Mol.Cell / Year: 2003
Title: Structural basis of the ribosomal machinery for Peptide bond formation, translocation, and nascent chain progression
Authors: Bashan, A. / Agmon, I. / Zarivatch, R. / Schluenzen, F. / Harms, J.M. / Berisio, R. / Bartels, H. / Franceschi, F. / Auerbach, T. / Hansen, H.A. / Kossoy, E. / Kessler, M. / Yonath, A.
History
DepositionJan 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: 23S ribosomal RNA
5: RNA ACC(Puromycin)


Theoretical massNumber of molelcules
Total (without water)934,8332
Polymers934,8332
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)169.9, 410.4, 697.1
Angle α, β, γ (deg.)90, 90, 90
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: RNA chain RNA ACC(Puromycin)


Mass: 1428.086 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: RNA chain of the sequence ACC. The terminal C was coupled via a phosphodiester bond to the 5 OH of the N6-dimethyl moiety of puromycin

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4 Å3/Da / Density % sol: 64 %
Crystal growpH: 7.8
Details: ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL; SOAKING CRYSTALS IN: 0.0125mM ACCP, pH 7.80
Components of the solutions
IDNameCrystal-IDSol-ID
1ETHANOL11
2DIMETHYLHEXANEDIOL11
3MGCL211
4KCL11
5NH4CL11
6HEPES11
7ETHANOL12
8DIMETHYLHEXANEDIOL12
9MGCL212
10KCL12
11NH4CL12
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
51
61
71
81
91
101
111

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9762
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 249369 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Rsym value: 0.156 / Net I/σ(I): 7.9
Reflection shellResolution: 3.7→3.76 Å / Mean I/σ(I) obs: 1.8 / Rsym value: 0.393 / % possible all: 97.3
Reflection
*PLUS
Highest resolution: 3.7 Å / Lowest resolution: 50 Å / Rmerge(I) obs: 0.156
Reflection shell
*PLUS
% possible obs: 97.3 % / Rmerge(I) obs: 0.393

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
CNSrefinement
CCP4phasing
Omodel building
RefinementMethod to determine structure: DIFFERENCE FOURIER MAPS
Starting model: PDB ENTRY 1NKW

1nkw


Resolution: 3.7→15 Å / Rfactor Rfree error: 0.003 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.297 12015 5 %random
Rwork0.283 ---
obs0.2831 240738 --
all-240738 --
Refinement stepCycle: LAST / Resolution: 3.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 59455 0 0 59455
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_d0.8
X-RAY DIFFRACTIONc_angle_deg0.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refinement
*PLUS
Rfactor Rfree: 0.305
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_d

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