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- PDB-1bgz: S8 RRNA BINDING SITE FROM E. COLI, NMR, 6 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1bgz
TitleS8 RRNA BINDING SITE FROM E. COLI, NMR, 6 STRUCTURES
ComponentsRNA
KeywordsRNA / RIBONUCLEIC ACID / 16S RRNA / INTERNAL LOOP / BASE TRIPLE
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsKalurachchi, K. / Nikonowicz, E.P.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: NMR structure determination of the binding site for ribosomal protein S8 from Escherichia coli 16 S rRNA.
Authors: Kalurachchi, K. / Nikonowicz, E.P.
#1: Journal: Biochim.Biophys.Acta / Year: 1979
Title: Binding Sites for Ribosomal Proteins S8 and S15 in the 16 S RNA of Escherichia Coli
Authors: Zimmermann, R.A. / Singh-Bergmann, K.
History
DepositionJun 3, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA


Theoretical massNumber of molelcules
Total (without water)7,3561
Polymers7,3561
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)6 / 50FEWEST RESTRAINT VIOLATIONS
Representative

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Components

#1: RNA chain RNA


Mass: 7356.392 Da / Num. of mol.: 1 / Fragment: 16S RRNA BINDING SITE FOR S8 / Source method: obtained synthetically / Details: RNA HAIRPIN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121CT-HSQC
131COSY
141HETCOR
NMR detailsText: 2D AND 3D DOUBLE AND TRIPLE RESONANCE EXPERIMENTS WERE USED TO OBTAIN DISTANCE AND TORSION ANGLE CONSTRAINTS.

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Sample preparation

DetailsContents: H2O/D2O
Sample conditionsIonic strength: 10mM NACL, 10mM POTASSIUM PHOSPHATE / pH: 6.8 / Pressure: AMBIENT / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX500 / Manufacturer: Bruker / Model: AMX500 / Field strength: 500 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: FEWEST RESTRAINT VIOLATIONS / Conformers calculated total number: 50 / Conformers submitted total number: 6

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