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- PDB-2be0: Complex Between Paromomycin Derivative JS5-39 and the 16S-Rrna A-Site. -

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Basic information

Entry
Database: PDB / ID: 2be0
TitleComplex Between Paromomycin Derivative JS5-39 and the 16S-Rrna A-Site.
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/antibiotic / RNA-AMINOGLYCOSIDE INTERACTIONS / A SITE / UOU PAIRS / AA BULGES / RNA-antibiotic complex
Function / homologyChem-JS5 / RNA / RNA (> 10)
Function and homology information
Biological speciesStreptomyces rimosus subsp. paromomycinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsFrancois, B. / Westhof, E.
CitationJournal: ANGEW.CHEM.INT.ED.ENGL. / Year: 2004
Title: Antibacterial aminoglycosides with a modified mode of binding to the ribosomal-RNA decoding site
Authors: Francois, B. / Szychowski, J. / Adhikari, S.S. / Pachamuthu, K. / Swayze, E.E. / Griffey, R.H. / Migawa, M.T. / Westhof, E. / Hanessian, S.
History
DepositionOct 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_molecule_features / struct_site
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Mar 13, 2024Group: Source and taxonomy / Category: pdbx_entity_src_syn / Item: _pdbx_entity_src_syn.entity_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)15,6084
Polymers14,0972
Non-polymers1,5122
Water79344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.141, 39.141, 99.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
DetailsThe biological assembly is the duplex

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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: 16S Rrna A Site
Source: (synth.) Streptomyces rimosus subsp. paromomycinus (bacteria)
#2: Chemical ChemComp-JS5 / (2S,3S,4R,5R,6R)-5-AMINO-2-(AMINOMETHYL)-6-((2R,3R,4R,5S)-5-((1R,2R,3S,5R,6S)-3,5-DIAMINO-2-((2S,3R,4R,5S,6R)-3-AMINO-4 ,5-DIHYDROXY-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-6-HYDROXYCYCLOHEXYLOXY)-2-(HYDROXYMETHYL)-4-(2-((R)-PIPERIDI N-3-YLMETHYLAMINO)ETHOXY)-TETRAHYDROFURAN-3-YLOXY)-TETRAHYDRO-2H-PYRAN-3,4-DIOL / 2"-O-[N-(3-(AMINOMETHYL)-PYRIDINE)-2-AMINOETHYL]PAROMOMYCIN / O-2-AMINO-2-DEOXY-ALPHA-D-GLUCOPYRANOSYL-(1,4)-O-[O-2,6-DIAMINO-2,6-DIDEOXY-BETA-L-IDOPYRANOSYL-(1,3)-BETA-D-2-O-(3-ETHY LAMINOMETHYL)-PYRIDYL-(1,5)]-2-DEOXY-D-STREPTAMINE


Mass: 755.855 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H61N7O14
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.69 Å3/Da / Density % sol: 54.34 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 6% MPD, 0.3M potassium chloride, 5% glycerol, 0.1M cacodylate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 310K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2potassium chloride11
3glycerol11
4cacodylateCacodylic acid11
5H2O11
6MPD12
7potassium chloride12
8cacodylateCacodylic acid12
9H2O12

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 13, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.63→50 Å / Num. all: 46641 / Num. obs: 46641 / % possible obs: 99 % / Observed criterion σ(I): 5 / Redundancy: 10 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 28
Reflection shellResolution: 2.63→2.72 Å / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 9.4 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J7T

1j7t


Resolution: 2.63→30 Å / σ(F): 2
Details: 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. reflectionSelection details
Rfree0.2665 3842 RANDOM
Rwork0.2236 --
all-4453 -
obs-4291 -
Refine analyzeLuzzati coordinate error obs: 0.42 Å / Luzzati sigma a obs: 0.52 Å
Refinement stepCycle: LAST / Resolution: 2.63→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 898 104 44 1046
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.023
X-RAY DIFFRACTIONc_dihedral_angle_d10.251
X-RAY DIFFRACTIONc_improper_angle_d1.241
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1dna-rna_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4JS5_39.param

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