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

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Basic information

Entry
Database: PDB / ID: 1njm
TitleThe crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with a tRNA acceptor stem mimic (ASM) and the antibiotic sparsomycin
Components
  • 23S ribosomal RNA
  • 50S ribosomal protein L16
  • GENERAL STRESS PROTEIN CTC
  • tRNA acceptor stem mimic
KeywordsRIBOSOME / Ribosomes / tRNA / puromycin / sparsomycin / peptidyl-transferase / peptide bond formation
Function / homology
Function and homology information


5S rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L16 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal ...Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L16 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L16 / : / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e
Similarity search - Domain/homology
SPARSOMYCIN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL16
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER MAPS / Resolution: 3.6 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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
5: tRNA acceptor stem mimic
K: 50S ribosomal protein L16
T: GENERAL STRESS PROTEIN CTC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)986,7005
Polymers986,3384
Non-polymers3611
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)169.6, 409.4, 695.1
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 tRNA acceptor stem mimic


Mass: 11391.945 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The terminal C of ASM was coupled via a phosphodiester bond to the 5 OH of the N6-dimethyl moiety of puromycin
#3: Protein 50S ribosomal protein L16 / / Coordinate model: Cα atoms only


Mass: 16125.997 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXJ5
#4: Protein GENERAL STRESS PROTEIN CTC / Coordinate model: Cα atoms only


Mass: 25415.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RX88
#5: Chemical ChemComp-SPS / SPARSOMYCIN / Sparsomycin


Mass: 361.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19N3O5S2

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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 growDetails: ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, SPARSOMYCIN; SOAKING CRYSTALS IN: 0.025mM ASM
Components of the solutions
IDNameCrystal-IDSol-ID
1ETHANOL11
2DIMETHYLHEXANEDIOL11
3MGCL211
4KCL11
5NH4CL11
6SPARSOMYCIN11
7HEPES11
8ETHANOL12
9DIMETHYLHEXANEDIOL12
10MGCL212
11KCL12
12NH4CL12
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion
Details: Harms, J.M., (2001) Cell (Cambridge,Mass.), 107, 679.
pH: 7.8
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
121

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Nov 9, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 290998 / % possible obs: 94.2 % / Observed criterion σ(I): -3 / Rsym value: 0.169 / Net I/σ(I): 5.8
Reflection shellResolution: 3.6→3.66 Å / Mean I/σ(I) obs: 1.7 / Rsym value: 0.356 / % possible all: 93.8
Reflection
*PLUS
% possible obs: 95.2 % / Rmerge(I) obs: 0.169
Reflection shell
*PLUS
% possible obs: 93.8 % / Rmerge(I) obs: 0.356

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Processing

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

1nkw


Resolution: 3.6→15 Å / Rfactor Rfree error: 0.003 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.308 12535 5 %random
Rwork0.284 ---
all0.2841 250710 --
obs0.2841 250710 --
Refinement stepCycle: LAST / Resolution: 3.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms347 59902 22 0 60271
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d0.98
X-RAY DIFFRACTIONc_angle_deg0.98
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: 0.326
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg0.97

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