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- PDB-225d: A TETRAMERIC DNA STRUCTURE WITH PROTONATED CYTOSINE:CYTOSINE BASE... -

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Basic information

Entry
Database: PDB / ID: 225d
TitleA TETRAMERIC DNA STRUCTURE WITH PROTONATED CYTOSINE:CYTOSINE BASE PAIRS
ComponentsDNA (5'-D(*TP*CP*CP*CP*CP*C)-3')
KeywordsDNA / INTERCALATED CYTOSINE TETRAD
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / MOLECULAR DYNAMICS, ENERGY MINIMIZATION
AuthorsGehring, K. / Leroy, J.L. / Gueron, M.
CitationJournal: Nature / Year: 1993
Title: A tetrameric DNA structure with protonated cytosine.cytosine base pairs.
Authors: Gehring, K. / Leroy, J.L. / Gueron, M.
History
DepositionJul 12, 1995Processing site: BNL
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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: DNA (5'-D(*TP*CP*CP*CP*CP*C)-3')
B: DNA (5'-D(*TP*CP*CP*CP*CP*C)-3')
C: DNA (5'-D(*TP*CP*CP*CP*CP*C)-3')
D: DNA (5'-D(*TP*CP*CP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,8214
Polymers6,8214
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 / -
Representative

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Components

#1: DNA chain
DNA (5'-D(*TP*CP*CP*CP*CP*C)-3')


Mass: 1705.145 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Keywords: DEOXYRIBONUCLEIC ACID

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: DATA COLLECTION PARAMETERS: FREQUENCY: 600 MHZ FOR 1H, 242 MHZ FOR 31P SAMPLE TUBE: 5 MM, 7.5 MILLIMOLAR STRAND, PH 4.3, 25 C SPECTRA FOR ASSIGNMENTS: HOMONUCLEAR PROTON 2D, 1H-31P TOCSY; ...Text: DATA COLLECTION PARAMETERS: FREQUENCY: 600 MHZ FOR 1H, 242 MHZ FOR 31P SAMPLE TUBE: 5 MM, 7.5 MILLIMOLAR STRAND, PH 4.3, 25 C SPECTRA FOR ASSIGNMENTS: HOMONUCLEAR PROTON 2D, 1H-31P TOCSY; SPECTRA FOR CONSTRAINTS: NOESY, DQF-COSY, 1H-31P COSY

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Sample preparation

Sample conditionspH: 4.3 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR softwareName: X-PLOR / Developer: BRUNGER / Classification: refinement
RefinementMethod: MOLECULAR DYNAMICS, ENERGY MINIMIZATION / Software ordinal: 1
Details: STRUCTURE CALCULATION: MOLECULAR DYNAMICS AND ENERGY MINIMIZATION USING X-PLOR CONSTRAINTS (PER STRAND): TOTAL 70 DISTANCE CONSTRAINTS (ABOUT 12/NUCLEOTIDE) 43 FROM INTRANUCLEOTIDE NOES 6 ...Details: STRUCTURE CALCULATION: MOLECULAR DYNAMICS AND ENERGY MINIMIZATION USING X-PLOR CONSTRAINTS (PER STRAND): TOTAL 70 DISTANCE CONSTRAINTS (ABOUT 12/NUCLEOTIDE) 43 FROM INTRANUCLEOTIDE NOES 6 FROM SEQUENTIAL INTERNUCLEOTIDE NOES 21 FROM NON-SEQUENTIAL INTERNUCLEOTIDE NOES 15 FROM HYDROGEN BONDS DIHEDRAL ANGLE CONSTRAINTS 10 BACKBONE AND SUGAR RING TORSION ANGLES CONSTRAINTS TO MAKE CYTOSINE BASE PAIRS PLANAR 4-FOLD SYMMETRY CONSTRAINTS (AS 3 SETS OF PAIRWISE NON-CRYSTALLOGRAPHIC SYMMETRY CONSTRAINTS)
NMR constraintsNOE constraints total: 70 / NOE intraresidue total count: 43 / NOE sequential total count: 6 / Hydrogen bond constraints total count: 15
NMR ensembleConformers submitted total number: 1

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