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- PDB-2tob: SOLUTION STRUCTURE OF THE TOBRAMYCIN-RNA APTAMER COMPLEX, NMR, 13... -

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Entry
Database: PDB / ID: 2tob
TitleSOLUTION STRUCTURE OF THE TOBRAMYCIN-RNA APTAMER COMPLEX, NMR, 13 STRUCTURES
ComponentsRNA (5'-R(*AP*CP*UP*UP*GP*GP*UP*UP*UP*AP*GP*GP*UP*AP*AP*UP*GP*AP*GP*U)-3')
KeywordsRNA / AMINOGLYCOSIDE-RNA RECOGNITION / TOBRAMYCIN
Function / homology1,3-DIAMINO-4,5,6-TRIHYDROXY-CYCLOHEXANE / 3-ammonio-3-deoxy-alpha-D-glucopyranose / Chem-TOC / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / DISTANCE-RESTRAINED MOLECULAR DYNAMICS
AuthorsJiang, L. / Patel, D.J.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: Solution structure of the tobramycin-RNA aptamer complex.
Authors: Jiang, L. / Patel, D.J.
History
DepositionJun 17, 1998Processing site: BNL
Revision 1.0Jun 22, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 24, 2020Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Source and taxonomy
Category: ndb_struct_na_base_pair / pdbx_database_status ...ndb_struct_na_base_pair / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref / struct_ref_seq
Item: _ndb_struct_na_base_pair.hbond_type_12 / _pdbx_database_status.process_site
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 1, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*AP*CP*UP*UP*GP*GP*UP*UP*UP*AP*GP*GP*UP*AP*AP*UP*GP*AP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9354
Polymers6,4271
Non-polymers5093
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)13 / 40LOWEST NOE AND TOTAL ENERGY
RepresentativeModel #1

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Components

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


Mass: 6426.815 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Sugar ChemComp-TOA / 3-ammonio-3-deoxy-alpha-D-glucopyranose / 3-DEOXY-3-AMINO GLUCOSE / 3-ammonio-3-deoxy-alpha-D-glucose / 3-ammonio-3-deoxy-D-glucose / 3-ammonio-3-deoxy-glucose


Type: D-saccharide, alpha linking / Mass: 180.179 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H14NO5
IdentifierTypeProgram
a-D-Glcp3NIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Sugar ChemComp-TOC / 2,6-diammonio-2,3,6-trideoxy-alpha-D-glucopyranose / 2,3,6-TRIDEOXY-2,6-DIAMINO GLUCOSE / 2,6-diammonio-2,3,6-trideoxy-alpha-D-glucose / 2,6-diammonio-2,3,6-trideoxy-D-glucose / 2,6-diammonio-2,3,6-trideoxy-glucose


Type: D-saccharide, alpha linking / Mass: 164.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H16N2O3
IdentifierTypeProgram
a-D-3-deoxy-GlcpN6NIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-2TB / 1,3-DIAMINO-4,5,6-TRIHYDROXY-CYCLOHEXANE


Mass: 164.203 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H16N2O3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
131HMQCNULL
NMR detailsText: D2O: 2D NOESY (50MS,120MS,200MS,300MS MIXING TIMES), PHASE-SENSITIVE COSY, TOCSY, 1H-13C HSQC, 3D NOESY-HMQC (120MS, 300MS MIXING TIMES), 3D HCCH-COSY, 3D HCCH-TOCSY (65MS), 2D HP CORRELATION, C13 FILTERED NOESY

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Sample preparation

DetailsContents: D(2)O/H(2)O
Sample conditionsIonic strength: 10mM NA(2)HPO(4) / pH: 6.1 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS5001
Varian UNITYPLUSVarianUNITYPLUS6002

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
VARIAN VNMRVNMRstructure solution
RefinementMethod: DISTANCE-RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST NOE AND TOTAL ENERGY / Conformers calculated total number: 40 / Conformers submitted total number: 13

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