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- PDB-1bdz: NMR STRUCTURE OF A 14 MER EXTENDED C-MYB COGNATE DNA SEQUENCE 5'D... -

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Basic information

Entry
Database: PDB / ID: 1bdz
TitleNMR STRUCTURE OF A 14 MER EXTENDED C-MYB COGNATE DNA SEQUENCE 5'D(APCPAPAP CPTPGPCP APGPTPTP GPT)3', MINIMIZED AVERAGE STRUCTURE
ComponentsDNA (5'-D(*AP*CP*AP*AP*CP*TP*GP*CP*AP*GP*TP*TP*GP*T)-3')
KeywordsDNA / DEOXYRIBONUCLEIC ACID / DUPLEX DNA / C-MYB COGNATE SITE
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / RELAXATION MATRIX, RESTRAINED MOLECULAR DYNAMICS CALCULATION
AuthorsRadha, P.K. / Patel, P.K. / Hosur, R.V.
CitationJournal: Biochemistry / Year: 1998
Title: NMR structure of the extended Myb cognate sequence and modeling studies on specific DNA-Myb complexes.
Authors: Radha, P.K. / Patel, P.K. / Hosur, R.V.
History
DepositionMay 12, 1998Processing site: BNL
Revision 1.0Dec 2, 1998Provider: 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

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*AP*CP*AP*AP*CP*TP*GP*CP*AP*GP*TP*TP*GP*T)-3')
B: DNA (5'-D(*AP*CP*AP*AP*CP*TP*GP*CP*AP*GP*TP*TP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)8,5602
Polymers8,5602
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)1 / 24GOOD R FACTOR (<0.21) AND LEAST DEVIATION IN COVALENT GEOMETRY
Representative

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Components

#1: DNA chain DNA (5'-D(*AP*CP*AP*AP*CP*TP*GP*CP*AP*GP*TP*TP*GP*T)-3')


Mass: 4279.804 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: CONTAINS C-MYB COGNATE SITE

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131ECOSY
141HMQC
NMR detailsText: THE STRUCTURE WAS DETERMINED USING NOESY, CLEAN TOCSY, ECOSY AND 2D HETERONUCLEAR INVERSE DETECTED 13C-1H HMQC SPECTRUM AT NATURAL ABUNDANCE.

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Sample preparation

DetailsContents: H2O
Sample conditionspH: 7 / Pressure: 0.1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3refinement
X-PLOR3phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3BRUNGERrefinement
UXNMRstructure solution
RefinementMethod: RELAXATION MATRIX, RESTRAINED MOLECULAR DYNAMICS CALCULATION
Software ordinal: 1
NMR ensembleConformer selection criteria: GOOD R FACTOR (<0.21) AND LEAST DEVIATION IN COVALENT GEOMETRY / Conformers calculated total number: 24 / Conformers submitted total number: 1

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