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- PDB-2o3x: Crystal Structure of the Prokaryotic Ribosomal Decoding Site Comp... -

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Basic information

Entry
Database: PDB / ID: 2o3x
TitleCrystal Structure of the Prokaryotic Ribosomal Decoding Site Complexed with Paromamine Derivative NB30
ComponentsRNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3')
KeywordsRNA / aminoglycoside / antibiotics / ribosome / decoding site / Prokaryote / Translation inhibition / Stop codon readthrough
Function / homologyChem-N30 / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKondo, J. / Hainrichson, M. / Nudelman, I. / Shallom-Shezifi, D. / Baasov, T. / Westhof, E.
CitationJournal: Chembiochem / Year: 2007
Title: Differential Selectivity of Natural and Synthetic Aminoglycosides towards the Eukaryotic and Prokaryotic Decoding A Sites.
Authors: Kondo, J. / Hainrichson, M. / Nudelman, I. / Shallom-Shezifi, D. / Barbieri, C.M. / Pilch, D.S. / Westhof, E. / Baasov, T.
History
DepositionDec 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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
A: RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3')
B: RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1653
Polymers14,7112
Non-polymers4541
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.140, 46.830, 85.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: RNA chain RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3')


Mass: 7355.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized
#2: Chemical ChemComp-N30 / (1R,2R,3S,4R,6S)-4,6-DIAMINO-2-[(5-AMINO-5-DEOXY-BETA-D-RIBOFURANOSYL)OXY]-3-HYDROXYCYCLOHEXYL 2-AMINO-2-DEOXY-ALPHA-D-GLUCOPYRANOSIDE


Mass: 454.473 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H34N4O10

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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: 2.26 Å3/Da / Density % sol: 45.59 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Sodium Cacodylate, Potassium chloride, 2-methyl-2,4-pentanediol, spermine tetrahydrochloride, glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Components of the solutions
IDNameCrystal-IDSol-ID
1Sodium Cacodylate11
2Potassium chloride11
32-methyl-2,4-pentanediol11
4spermine tetrahydrochloride11
5glycerol11
6Sodium Cacodylate12
7Potassium chloride12
82-methyl-2,4-pentanediol12
9spermine tetrahydrochloride12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9737 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 22, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9737 Å / Relative weight: 1
ReflectionResolution: 2.9→42.86 Å / Num. obs: 3222 / % possible obs: 99.4 % / Redundancy: 6.53 % / Rmerge(I) obs: 0.163 / Χ2: 0.94 / Net I/σ(I): 8.3 / Scaling rejects: 159
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.9-36.930.35322663270.57100
3-3.126.770.2892.520933090.34100
3.12-3.276.860.259320923050.35100
3.27-3.446.750.2443.821533190.5100
3.44-3.656.820.2395.121963220.81100
3.65-3.946.70.2495.521033140.84100
3.94-4.336.610.2176.321353220.9499.7
4.33-4.966.30.1749.220413221.34100
4.96-6.245.90.1511420083371.5100
6.24-42.865.760.07132.921053452.4795.3

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Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata processing
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
CrystalCleardata reduction
CrystalCleardata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J7T

1j7t


Resolution: 2.9→10 Å / FOM work R set: 0.756
Isotropic thermal model: G. Parkinson, J. Vojtechovsky, L. Clowney, A.T. Brunger, H.M. Berman, New Parameters for the Refinement of Nucleic Acid Containing Structures, Acta Cryst. D, 52, 57-64 (1996).
σ(F): 3
RfactorNum. reflection% reflection
Rfree0.285 292 9.3 %
Rwork0.246 --
obs-2948 93.8 %
Solvent computationBsol: 47.316 Å2
Displacement parametersBiso mean: 76.921 Å2
Baniso -1Baniso -2Baniso -3
1-13.647 Å20 Å20 Å2
2--2.852 Å20 Å2
3----16.499 Å2
Refinement stepCycle: LAST / Resolution: 2.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 898 31 0 929
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0071.5
X-RAY DIFFRACTIONc_angle_deg1.2342
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.9-3.030.456320.367285317
3.03-3.180.243210.311313334
3.18-3.380.414420.322320362
3.38-3.620.314370.274307344
3.62-3.970.375460.285336382
3.97-4.50.302450.254340385
4.5-5.50.269340.227370404
5.5-100.226350.185385420
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION2nb30_xplor.paramnb30_xplor.top
X-RAY DIFFRACTION3water.paramwater.top

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