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- PDB-106d: Solution structures of the i-motif tetramers of D(TCC), D(5MCCT) ... -

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Basic information

Entry
Database: PDB / ID: 106d
TitleSolution structures of the i-motif tetramers of D(TCC), D(5MCCT) and D(T5MCC). Novel NOE connections between amino protons and sugar protons
ComponentsDNA (5'-D(*MCYP*CP*T)-3')
KeywordsDNA
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR
AuthorsLeroy, J.-L. / Gueron, M.
CitationJournal: Structure / Year: 1995
Title: Solution structures of the i-motif tetramers of d(TCC), d(5methylCCT) and d(T5methylCC): novel NOE connections between amino protons and sugar protons.
Authors: Leroy, J.L. / Gueron, M.
History
DepositionDec 22, 1994Processing site: BNL
Revision 1.0Feb 7, 1995Provider: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag
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: DNA (5'-D(*MCYP*CP*T)-3')
B: DNA (5'-D(*MCYP*CP*T)-3')
C: DNA (5'-D(*MCYP*CP*T)-3')
D: DNA (5'-D(*MCYP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)3,0874
Polymers3,0874
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Atom site foot note1: SOME OF THE CYTIDINES ARE PROTONATED AT THE N3 POSITION. THESE RESIDUES HAVE BEEN ASSIGNED THE RESIDUE NAME C IN THE ENTRY AND ATOM H3 HAS BEEN FOOTNOTED.
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)8 / -
Representative

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Components

#1: DNA chain
DNA (5'-D(*MCYP*CP*T)-3')


Mass: 771.646 Da / Num. of mol.: 4 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementSoftware ordinal: 1
Details: 5MC STANDS FOR 5-METHYLCYTIDINE. THE STRUCTURE IS FORMED OF FOUR EQUIVALENT 5MCCT STRANDS DESIGNATED A, B, C, D. STRANDS A AND C, CONNECTED BY TWO HEMI-PROTONATED BASE PAIRS (5MC1.5MC1+ AND ...Details: 5MC STANDS FOR 5-METHYLCYTIDINE. THE STRUCTURE IS FORMED OF FOUR EQUIVALENT 5MCCT STRANDS DESIGNATED A, B, C, D. STRANDS A AND C, CONNECTED BY TWO HEMI-PROTONATED BASE PAIRS (5MC1.5MC1+ AND C2.C2+), FORM A PARALLEL-STRANDED DUPLEX. THE RELATION BETWEEN STRANDS B AND D IS THE SAME AS THAT BETWEEN STRANDS A AND C. THE STRANDS OF EACH DUPLEX ARE RELATED BY A LONGITUDINAL TWO-FOLD SYMMETRY AXIS. THE DUPLEXES HAVE THE SAME LONGITUDINAL AXIS, AND THEY ARE ANTI-PARALLEL. THEIR HEMI-PROTONATED C.C+ BASE PAIRS ARE INTERCALATED FACE-TO-FACE. THE DUPLEXES CAN BE TRANSFORMED INTO ONE ANOTHER BY A 180 DEGREE ROTATION AROUND A TWO-FOLD AXIS PERPENDICULAR TO THE LONGITUDINAL AXIS, AND CONSEQUENTLY AROUND A THIRD AXIS PERPENDICULAR TO THE FIRST TWO. THE H3 IMINO PROTONS OF THE HEMI-PROTONATED 5MC1.5MC1+ PAIRS WERE NOT INCORPORATED IN THE COMPUTATIONS. THOSE OF THE C2.C2+ PAIRS WERE ARBITRARILY LOCATED ON THE C2 RESIDUES OF STRANDS A AND B, RESPECTIVELY.
NMR ensembleConformers submitted total number: 8

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