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- PDB-1tob: SACCHARIDE-RNA RECOGNITION IN AN AMINOGLYCOSIDE ANTIBIOTIC-RNA AP... -

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Basic information

Entry
Database: PDB / ID: 1tob
TitleSACCHARIDE-RNA RECOGNITION IN AN AMINOGLYCOSIDE ANTIBIOTIC-RNA APTAMER COMPLEX, NMR, 7 STRUCTURES
ComponentsRNA (5'-R(GGCACGAGGUUUAGCUACACUCGUGCC)-3')
KeywordsRNA / RIBONUCLEIC ACID
Function / homology3-ammonio-3-deoxy-alpha-D-glucopyranose / 1,3-DIAMINO-5,6-DIHYDROXYCYCLOHEXANE / Chem-TOC / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / RESTRAINED MOLECULAR DYNAMICS
AuthorsJiang, L. / Suri, A.K. / Fiala, R. / Patel, D.J.
CitationJournal: Chem.Biol. / Year: 1997
Title: Saccharide-RNA recognition in an aminoglycoside antibiotic-RNA aptamer complex.
Authors: Jiang, L. / Suri, A.K. / Fiala, R. / Patel, D.J.
History
DepositionDec 12, 1996Processing site: BNL
Revision 1.0Jun 16, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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_step / pdbx_database_status ...ndb_struct_na_base_pair_step / 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_step.inclination / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag
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 ...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_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(GGCACGAGGUUUAGCUACACUCGUGCC)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1344
Polymers8,6411
Non-polymers4933
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)7 / 50ENERGY (INCLUDING RESTRAINT ENERGY TERM)
Representative

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Components

#1: RNA chain RNA (5'-R(GGCACGAGGUUUAGCUACACUCGUGCC)-3')


Mass: 8641.168 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-TOB / 1,3-DIAMINO-5,6-DIHYDROXYCYCLOHEXANE


Mass: 148.203 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H16N2O2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditionspH: 6.8 / 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
X-PLOR3.1structure solution
RefinementMethod: RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1 / Details: RESTRAINED MOLECULAR DYNAMICS.
NMR ensembleConformer selection criteria: ENERGY (INCLUDING RESTRAINT ENERGY TERM)
Conformers calculated total number: 50 / Conformers submitted total number: 7

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