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- PDB-2o3y: Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decod... -

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Basic information

Entry
Database: PDB / ID: 2o3y
TitleCrystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site in Presence of Paromamine Derivative NB30
ComponentsRNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3')
KeywordsRNA / aminoglycoside / antibiotics / ribosome / decoding site / Homo sapiens / Eukaryote / cytoplasmic / Translation inhibition / Stop codon readthrough
Function / homologySPERMINE / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3')
B: RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9133
Polymers14,7112
Non-polymers2021
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.940, 49.230, 57.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-77-

HOH

21A-78-

HOH

31B-49-

HOH

41B-68-

HOH

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Components

#1: RNA chain RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*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-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 46.63 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Sodium Cacodylate, Potassium chloride, 2-methyl-2,4-pentanediol, hexammine cobalt chloride, spermine tetrahydrochloride , 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
4hexammine cobalt chloride11
5spermine tetrahydrochloride11
6Sodium Cacodylate12
7Potassium chloride12
82-methyl-2,4-pentanediol12
9hexammine cobalt chloride12
10spermine tetrahydrochloride12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 2, 2006
RadiationMonochromator: horizontally side diffracting Silicon 111 crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.7→37.38 Å / Num. obs: 3818 / % possible obs: 94.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.086 / Χ2: 1 / Net I/σ(I): 7.8 / Scaling rejects: 99
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.7-2.83.50.3872.713363821.1596.7
2.8-2.913.480.2593.413003701.295.1
2.91-3.043.50.1314.713453811.1397.2
3.04-3.23.440.1255.413213821.0696.7
3.2-3.43.440.1216.212893741.1395.9
3.4-3.663.410.095712833760.9794.9
3.66-4.033.460.0819.513313810.9394.3
4.03-4.613.440.0938.413033780.8593.8
4.61-5.813.310.0910.913013900.8493.3
5.81-37.383.090.03720.612854040.7690

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Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata processing
CNSrefinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FQN

2fqn


Resolution: 2.7→30 Å / FOM work R set: 0.761 / σ(F): 3
Stereochemistry target values: 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).
RfactorNum. reflection% reflection
Rfree0.282 324 8 %
Rwork0.245 --
obs-3235 80.3 %
Solvent computationBsol: 50.512 Å2
Displacement parametersBiso mean: 64.225 Å2
Baniso -1Baniso -2Baniso -3
1--3.125 Å20 Å20 Å2
2---25.98 Å20 Å2
3---29.105 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 918 14 56 988
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0051.5
X-RAY DIFFRACTIONc_angle_deg12
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
2.7-2.820.432380.41253291
2.82-2.970.44340.353317351
2.97-3.160.342290.21328357
3.16-3.40.275450.301370415
3.4-3.740.282480.239375423
3.74-4.280.291400.178392432
4.28-5.390.256410.21430471
5.39-300.254490.268446495
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1dna-rna_rep.param
X-RAY DIFFRACTION2spm_xplor.param2
X-RAY DIFFRACTION3water_rep.param

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