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- PDB-1lc4: Crystal Structure of Tobramycin Bound to the Eubacterial 16S rRNA... -

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Basic information

Entry
Database: PDB / ID: 1lc4
TitleCrystal Structure of Tobramycin Bound to the Eubacterial 16S rRNA A Site
Components5'-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 / Antibiotic-RNA complex / adenine bulges
Function / homologyTOBRAMYCIN / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsVicens, Q. / Westhof, E.
Citation
Journal: Chem.Biol. / Year: 2002
Title: Crystal Structure of a Complex between the Aminoglycoside Tobramycin and an Oligonucleotide Containing the Ribosomal Decoding A Site
Authors: Vicens, Q. / Westhof, E.
#1: Journal: Structure / Year: 2001
Title: Crystal Structure of Paromomycin Docked into the Eubacterial Ribosomal Decoding A Site
Authors: Vicens, Q. / Westhof, E.
History
DepositionApr 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 8, 2012Group: Derived calculations
Revision 1.4Aug 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

Downloads & links

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Assembly

Deposited unit
A: 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: 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)15,6464
Polymers14,7112
Non-polymers9352
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.900, 32.800, 52.000
Angle α, β, γ (deg.)90.00, 107.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain 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: eubacterial 16S RRNA A SITE
#2: Chemical ChemComp-TOY / TOBRAMYCIN / 4-AMINO-2-[4,6-DIAMINO-3-(3-AMINO-6-AMINOMETHYL-5-HYDROXY-TETRAHYDRO-PYRAN-2-YLOXY)-2-HYDROXY-CYCLOHEXYLOXY]-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,5-DIOL


Mass: 467.514 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H37N5O9 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.59 Å3/Da / Density % sol: 52.46 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: MPD, sodium cacodylate, sodium chloride, potassium chloride, magnesium sulfate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 310K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2sodium cacodylate11
3NaCl11
4KCl11
5MgSO411
6MPD12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.75-2 %1drop
20.5-1 %glycerol1drop
32.2-2.3 mMtobramycin1drop
456.25-131.25 mM1dropor KClNaCl
562.5 mMsodium cacodylate1droppH6.4
60.5-1.55 mMRNA1drop
72.5 mM1dropMgSO4
840 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 24, 2001
Details: double crystal monochromator and toroidal focusing mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.54→10 Å / Num. all: 4899 / % possible obs: 95.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 62.8 Å2 / Rsym value: 0.059 / Net I/σ(I): 19.5
Reflection shellResolution: 2.54→2.64 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 9.2 / Num. unique all: 479 / Rsym value: 0.133 / % possible all: 98.4
Reflection
*PLUS
Lowest resolution: 10 Å / Num. obs: 4899 / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
% possible obs: 98.4 % / Rmerge(I) obs: 0.133

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J7T

1j7t


Resolution: 2.54→10 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1338987.24 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 1.5
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% reflectionSelection details
Rfree0.264 396 8.5 %random
Rwork0.214 ---
all-4899 --
obs-4644 91.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.7193 Å2 / ksol: 0.284702 e/Å3
Displacement parametersBiso mean: 61.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.54→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 898 64 76 1038
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005567
X-RAY DIFFRACTIONc_angle_deg1.03474
X-RAY DIFFRACTIONc_dihedral_angle_d9.71789
X-RAY DIFFRACTIONc_improper_angle_d0.75231
LS refinement shellResolution: 2.54→2.7 Å / Rfactor Rfree error: 0.058 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.426 53 7.8 %
Rwork0.314 629 -
obs--82.5 %
Refinement
*PLUS
Lowest resolution: 10 Å / % reflection Rfree: 7.5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg9.71789
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75231

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