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Basic information

Entry
Database: PDB / ID: 2pwt
TitleCrystal structure of the bacterial ribosomal decoding site complexed with aminoglycoside containing the L-HABA group
Components22-mer of the ribosomal decoding site
KeywordsRNA/ANTIBIOTIC / aminoglycoside / haba group / ribosomal decoding site / X-ray analysis / RNA / RNA-ANTIBIOTIC complex
Function / homologyDOUBLY FUNCTIONALIZED PAROMOMYCIN PM-II-162 / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKondo, J. / Pachamuthu, K. / Francois, B. / Szychowski, J. / Hanessian, S. / Westhof, E.
CitationJournal: Chemmedchem / Year: 2007
Title: Crystal Structure of the Bacterial Ribosomal Decoding Site Complexed with a Synthetic Doubly Functionalized Paromomycin Derivative: a New Specific Binding Mode to an A-Minor Motif Enhances in ...Title: Crystal Structure of the Bacterial Ribosomal Decoding Site Complexed with a Synthetic Doubly Functionalized Paromomycin Derivative: a New Specific Binding Mode to an A-Minor Motif Enhances in vitro Antibacterial Activity
Authors: Kondo, J. / Pachamuthu, K. / Francois, B. / Szychowski, J. / Hanessian, S. / Westhof, E.
History
DepositionMay 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_molecule_features / 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 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Mar 13, 2024Group: Source and taxonomy / Category: pdbx_entity_src_syn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 22-mer of the ribosomal decoding site
B: 22-mer of the ribosomal decoding site
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0785
Polymers13,4862
Non-polymers2,5923
Water3,711206
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.490, 43.020, 98.750
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 22-mer of the ribosomal decoding site


Mass: 6743.077 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized
#2: Chemical ChemComp-LHA / DOUBLY FUNCTIONALIZED PAROMOMYCIN PM-II-162 / (2S)-4-AMINO-N-[(1R,2S,3R,4R,5S)-5-AMINO-4-[(2-AMINO-2-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-3-{[3-O-(2,6-DIAMINO-2,6-DIDEO XY-BETA-L-IDOPYRANOSYL)-2-O-{2-[(2-PHENYLETHYL)AMINO]ETHYL}-BETA-D-RIBOFURANOSYL]OXY}-2-HYDROXYCYCLOHEXYL]-2-HYDROXYBUTA NAMIDE


Mass: 863.949 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C37H65N7O16
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.79 Å3/Da / Density % sol: 55.99 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 50 mM Na Cacodylate (pH 6.4), 150 mM KCl, 1% Glycerol, 1% 2-methyl-2,4-pentandiol, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 310K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2KCl11
3Glycerol11
4sodium Cacodylate11
5MPD12
6KCl12
7Glycerol12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.8→32.4 Å / Num. obs: 14605 / % possible obs: 100 % / Redundancy: 19.1 % / Rmerge(I) obs: 0.07
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.609

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J7T

1j7t


Resolution: 1.8→32 Å / σ(F): 0
Stereochemistry target values: Parkinson et al Acta Cryst. D52, 57 (1996)
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2272 15.5 %random
Rwork0.211 ---
obs-14603 99.9 %-
Solvent computationBsol: 38.111 Å2
Displacement parametersBiso mean: 37.822 Å2
Baniso -1Baniso -2Baniso -3
1--2.204 Å20 Å20 Å2
2--2.918 Å20 Å2
3----0.714 Å2
Refinement stepCycle: LAST / Resolution: 1.8→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 900 180 206 1286
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0061.5
X-RAY DIFFRACTIONc_angle_deg0.92
X-RAY DIFFRACTIONc_improper_angle_d1.3
X-RAY DIFFRACTIONc_mcbond_it1.6641.5
X-RAY DIFFRACTIONc_mcangle_it2.382
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3LHA_xplor.param
X-RAY DIFFRACTION4LHA_xplor.param

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