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- PDB-1j7t: Complex between Paromomycin and the 16S-rRNA A-site at 2.5 A reso... -

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Basic information

Entry
Database: PDB / ID: 1j7t
TitleComplex between Paromomycin and the 16S-rRNA A-site at 2.5 A resolution
Components5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'
KeywordsRNA / RNA-aminoglycoside interactions / A site / UoU pairs / AA bulges
Function / homologyPAROMOMYCIN / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsVicens, Q. / Westhof, E.
CitationJournal: Structure / Year: 2001
Title: Crystal structure of paromomycin docked into the eubacterial ribosomal decoding A site.
Authors: Vicens, Q. / Westhof, E.
History
DepositionMay 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-R(*CP*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(*CP*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)15,3284
Polymers14,0972
Non-polymers1,2312
Water97354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.000, 45.900, 95.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 7048.259 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Escherichia coli 16S rRNA A site
#2: Chemical ChemComp-PAR / PAROMOMYCIN / PAROMOMYCIN I / AMMINOSIDIN / CATENULIN / CRESTOMYCIN / MONOMYCIN A / NEOMYCIN E


Mass: 615.628 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H45N5O14 / Comment: Antimicrobial, medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.56 Å3/Da / Density % sol: 51.95 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: MPD, NaCl, MgSO4, glycerol, Na cacodylate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 310K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2NaCl11
3MgSO411
4glycerol11
5sodium cacodylate11
6MPD12
Crystal grow
*PLUS
Temperature: 21 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.75-2.5 %1drop
20.5-1 %glycerol1drop
32 mMparomomycin1drop
456.25-131.25 mM1dropNaCl
52.5-7.5 mM1dropMgSO4
662.5 mMsodium cacodylate1droppH6.4
70.5 mMRNA1drop
840-60 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 28, 2000
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.5→15 Å / Num. all: 5144 / Num. obs: 5144 / % possible obs: 95 % / Redundancy: 9.7 % / Rsym value: 0.055 / Net I/σ(I): 24.4
Reflection shellResolution: 2.5→2.59 Å / Mean I/σ(I) obs: 6.5 / Rsym value: 0.23 / % possible all: 97.4
Reflection
*PLUS
Lowest resolution: 10 Å / Num. obs: 5278 / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
% possible obs: 97.4 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 6.4

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Model containing the 16S rRNA A site as solved in the crystallographic structure of the 30S ribosomal particle complexed to paromomycin

Resolution: 2.5→15 Å / Isotropic thermal model: isotropic / 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
Rfree0.247 395 -random
Rwork0.206 ---
all-5278 --
obs-4772 90.4 %-
Displacement parametersBiso mean: 52.7 Å2
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 898 84 54 1036
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011222
X-RAY DIFFRACTIONc_angle_deg1.64474
X-RAY DIFFRACTIONc_dihedral_angle_d10.12787
X-RAY DIFFRACTIONc_improper_angle_d1.5716
Refinement
*PLUS
Lowest resolution: 10 Å / % reflection Rfree: 7.5 % / Rfactor obs: 0.206 / Rfactor Rfree: 0.247 / Rfactor Rwork: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg10.12787
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.5716

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