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- PDB-1cs2: NMR STRUCTURES OF B-DNA D(CTACTGCTTTAG).D(CTAAAGCAGTAG) -

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Basic information

Entry
Database: PDB / ID: 1cs2
TitleNMR STRUCTURES OF B-DNA D(CTACTGCTTTAG).D(CTAAAGCAGTAG)
Components
  • 5'-d(*CP*TP*AP*AP*AP*GP*CP*AP*GP*TP*AP*G)-3'
  • 5'-d(*CP*TP*AP*CP*TP*GP*CP*TP*TP*TP*AP*G)-3'
KeywordsDNA / DOUBLE HELIX / MODELLING PROTOCOLS
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / MOLECULAR DYNAMICS, MATRIX RELAXATION
AuthorsLeporc, S. / Mauffret, O. / Tevanian, G. / Lescot, E. / Monnot, M. / Fermandjian, S.
CitationJournal: Nucleic Acids Res. / Year: 1999
Title: An NMR and molecular modelling analysis of d(CTACTGCTTTAG). d(CTAAAGCAGTAG) reveals that the particular behaviour of TpA steps is related to edge-to-edge contacts of their base-pairs in the major groove
Authors: Leporc, S. / Mauffret, O. / Tevanian, G. / Lescot, E. / Monnot, M. / Fermandjian, S.
History
DepositionAug 16, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-d(*CP*TP*AP*CP*TP*GP*CP*TP*TP*TP*AP*G)-3'
B: 5'-d(*CP*TP*AP*AP*AP*GP*CP*AP*GP*TP*AP*G)-3'


Theoretical massNumber of molelcules
Total (without water)7,3242
Polymers7,3242
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)3 / 22back calculated data agree with experimental NOESY spectrum
Representative

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Components

#1: DNA chain 5'-d(*CP*TP*AP*CP*TP*GP*CP*TP*TP*TP*AP*G)-3'


Mass: 3628.377 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-d(*CP*TP*AP*AP*AP*GP*CP*AP*GP*TP*AP*G)-3'


Mass: 3695.443 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
1112D NOESY
121P-COSY
1312D 31P/1H HETEROTOCSY
2422D NOESY

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Sample preparation

Details
Solution-IDContents
14 MM DNA DUPLEX, 0.4 ML POTASSIUM DIHYDROGEN PHOSPHATE DISODIUM HYDROGEM PHOSPHATE BUFFER; 100% D2O
24 MM DNA DUPLEX, 0.4 ML POTASSIUM DIHYDROGEN PHOSPHATE DISODIUM HYDROGEM PHOSPHATE BUFFER; 90% H2O, 10%D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.1 6.9 AMBIENT 308 K
20.1 6.9 AMBIENT 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker AMXBrukerAMX5002

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Processing

NMR software
NameVersionDeveloperClassification
JUMNA10.1LAVERYstructure calculation
X-PLOR3.1BRUNGERstructure calculation
Felix97MSIdata analysis
XwinNMR2BRUKERcollection
X-PLOR3.1BRUNGERrefinement
RefinementMethod: MOLECULAR DYNAMICS, MATRIX RELAXATION / Software ordinal: 1
Details: MODEL 1: AVERAGE OF THE EIGHT STRUCTURES OBTAINED WITH JUMNA AND AMBER94 AS FORCE FIELD. MODEL 2: AVERAGE OF THE EIGHT STRUCTURES OBTAINED WITH JUMNA AND FLEX AS FORCE FIELD. MODEL 3: ...Details: MODEL 1: AVERAGE OF THE EIGHT STRUCTURES OBTAINED WITH JUMNA AND AMBER94 AS FORCE FIELD. MODEL 2: AVERAGE OF THE EIGHT STRUCTURES OBTAINED WITH JUMNA AND FLEX AS FORCE FIELD. MODEL 3: AVERAGE OF THE SIX STRUCTURES OBTAINED WITH X- PLOR.
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 22 / Conformers submitted total number: 3

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