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- PDB-1skp: NMR STRUCTURE OF D(GCATATGATAG)(DOT)D(CTATCATATGC): A CONSENSUS S... -

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Basic information

Entry
Database: PDB / ID: 1skp
TitleNMR STRUCTURE OF D(GCATATGATAG)(DOT)D(CTATCATATGC): A CONSENSUS SEQUENCE FOR PROMOTERS RECOGNIZED BY SIGMA-K RNA POLYMERASE, 4 STRUCTURES
Components(SIGMA-K RNA POLYMERASE CONSENSUS SEQUENCE) x 2
KeywordsDNA / PROMOTER SEQUENCE
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / MOLECULAR DYNAMIC (RMD), MONTE CARLO (RMC) CALCULATIONS
AuthorsTonelli, M. / Ragg, E. / Bianucci, A.M. / Lesiak, K. / James, T.L.
CitationJournal: Biochemistry / Year: 1998
Title: Nuclear magnetic resonance structure of d(GCATATGATAG). d(CTATCATATGC): a consensus sequence for promoters recognized by sigma K RNA polymerase.
Authors: Tonelli, M. / Ragg, E. / Bianucci, A.M. / Lesiak, K. / James, T.L.
History
DepositionMay 20, 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 1.3Mar 2, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SIGMA-K RNA POLYMERASE CONSENSUS SEQUENCE
B: SIGMA-K RNA POLYMERASE CONSENSUS SEQUENCE


Theoretical massNumber of molelcules
Total (without water)6,7052
Polymers6,7052
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)4 / 20CONVERGENCE, R FACTORS, ENERGIES
Representative

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Components

#1: DNA chain SIGMA-K RNA POLYMERASE CONSENSUS SEQUENCE


Mass: 3397.247 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain SIGMA-K RNA POLYMERASE CONSENSUS SEQUENCE


Mass: 3308.185 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
NMR detailsText: STRUCTURE DETERMINED WITH HOMONUCLEAR NMR METHODS.

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Sample preparation

DetailsContents: H2O AND D2O
Sample conditionsIonic strength: 0.5 M / pH: 7.0 / Pressure: 1 ATMOSPHERE / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX600 / Manufacturer: Bruker / Model: AMX600 / Field strength: 600 MHz

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Processing

SoftwareName: AMBER / Classification: refinement
NMR software
NameDeveloperClassification
MARDIGRASPEARLMANrefinement
MARDIGRASstructure solution
Amberstructure solution
DNAminiCarlostructure solution
RefinementMethod: MOLECULAR DYNAMIC (RMD), MONTE CARLO (RMC) CALCULATIONS
Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE BIOCHEMISTRY CITATION ABOVE. MODEL 1 : REFINED BY RMD FROM A-DNA MODEL 2 : REFINED BY RMD FROM B-DNA MODEL 3 : REFINED BY RMC FROM A-DNA MODEL 4 : REFINED BY RMC FROM B-DNA
NMR ensembleConformer selection criteria: CONVERGENCE, R FACTORS, ENERGIES
Conformers calculated total number: 20 / Conformers submitted total number: 4

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