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- PDB-139d: SOLUTION STRUCTURE OF A PARALLEL-STRANDED G-QUADRUPLEX DNA -

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Basic information

Entry
Database: PDB / ID: 139d
TitleSOLUTION STRUCTURE OF A PARALLEL-STRANDED G-QUADRUPLEX DNA
ComponentsDNA (5'-D(*TP*TP*GP*GP*GP*GP*T)-3')
KeywordsDNA / G-QUADRUPLEX / ANTI GLYCOSIDIC TORSION ANGLES
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / DISTANCE GEOMETRY, MOLECULAR DYNAMICS
AuthorsPatel, D.J. / Wang, Y.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Solution structure of a parallel-stranded G-quadruplex DNA.
Authors: Wang, Y. / Patel, D.J.
#1: Journal: Biochemistry / Year: 1992
Title: Guanine Residues in D(T2Ag3) and D(T2G4) Form Parallel-Stranded Potassium Cation Stabilized G-Quadruplexes with Anti Glycosidic Torsion Angles in Solution
Authors: Wang, Y. / Patel, D.J.
History
DepositionSep 28, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)8,7384
Polymers8,7384
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)4 / 7structures with the least restraint violations,structures with the lowest energy
Representative

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Components

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


Mass: 2184.444 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

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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
NMR softwareName: X-PLOR / Developer: BRUNGER / Classification: refinement
RefinementMethod: DISTANCE GEOMETRY, MOLECULAR DYNAMICS / Software ordinal: 1
Details: RESTRAINED MOLECULAR DYNAMICS CALCULATIONS WERE DONE ON A MOLECULAR MODEL BUILT TO QUALITATIVELY FIT THE NMR DATA. THE REFINEMENT WAS CONDUCTED IN TWO STAGES. IN THE FIRST STAGE, SEVEN ...Details: RESTRAINED MOLECULAR DYNAMICS CALCULATIONS WERE DONE ON A MOLECULAR MODEL BUILT TO QUALITATIVELY FIT THE NMR DATA. THE REFINEMENT WAS CONDUCTED IN TWO STAGES. IN THE FIRST STAGE, SEVEN STRUCTURES WERE CALCULATED USING DISTANCE RESTRAINTS (WITH DIFFERENT SEEDS FOR INITIAL VELOCITY ASSIGNMENTS). IN THE SECOND STAGE, FOUR OF THE SEVEN DISTANCE-REFINED STRUCTURES WERE REFINED FURTHER BY NOE INTENSITY-RESTRAINED MOLECULAR DYNAMICS CALCULATIONS. THE R(1/6) VALUE WAS USED TO MONITOR THE REFINEMENT DURING THE SECOND STAGE. THE FINAL R(1/6) VALUES FOR THE FOUR AVERAGED MINIMIZED STRUCTURES WERE BETWEEN 0.025 AND 0.033. RMS DEVIATIONS FROM IDEALIZED GEOMETRY FOR THE TWO AVERAGED MINIMIZED STRUCTURES ARE AS FOLLOWS: MODEL1 MODEL2 MODEL3 MODEL4 BOND (ANGSTROMS) 0.013 0.013 0.012 0.011 ANGLES (DEGREES) 2.713 2.634 2.731 2.728 IMPROPERS (DEGREES) 0.476 0.560 0.242 0.280. THE STRUCTURE HAS AN APPROXIMATE FOUR-FOLD SYMMETRY RELATING THE FOUR STRANDS WITH THE SYMMETRY AXIS COINCIDENT WITH THE HELICAL AXIS. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. IT WILL ALSO YIELD APPROXIMATE COORDINATES FOR CHAIN *C* WHEN APPLIED TO CHAIN *B* AND WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *D* WHEN APPLIED TO CHAIN *C*.
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 7 / Conformers submitted total number: 4

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