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- PDB-1a6h: DNA QUADRUPLEX CONTAINING GCGC TETRAD, NMR, 4 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1a6h
TitleDNA QUADRUPLEX CONTAINING GCGC TETRAD, NMR, 4 STRUCTURES
ComponentsDNA (5'-D(GP*CP*GP*GP*TP*TP*TP*GP*CP*GP*G)-3')
KeywordsDNA / DEOXYRIBONUCLEIC ACID / DNA QUADRUPLEX / FRAGILE X SYNDROME / D(CGG) TRIPLET REPEAT / GCGC TETRADS
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / DISTANCE GEOMETRY, RESTRAINED MOLECULAR DYNAMICS
AuthorsKettani, A. / Kumar, R.A. / Patel, D.J.
CitationJournal: J.Mol.Biol. / Year: 1995
Title: Solution structure of a DNA quadruplex containing the fragile X syndrome triplet repeat.
Authors: Kettani, A. / Kumar, R.A. / Patel, D.J.
History
DepositionFeb 25, 1998Processing site: BNL
SupersessionJun 17, 1998ID: 228D
Revision 1.0Jun 17, 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: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name
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(GP*CP*GP*GP*TP*TP*TP*GP*CP*GP*G)-3')
B: DNA (5'-D(GP*CP*GP*GP*TP*TP*TP*GP*CP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)6,8422
Polymers6,8422
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 / 4ALL CONFORMERS PRESENTED
Representative

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Components

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


Mass: 3421.219 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111IN D(2)O: NOESY
121COSY-45
131COSY-90
141TOCSY
151(1)H-(31)P COSY
161(1H)-(13)C HMQC. NOESY BUILDUP AT 50
171100
181150
191200 AND 300 ; IN H(2)O: NOESY (80 AND 250 MS)
1101(1)H-(15)N HMQC

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Sample preparation

Sample conditionspH: 6.5 / Temperature: 317 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VARIAN UNITY PLUSVarianVARIAN UNITY PLUS5001
Varian VARIAN UNITY PLUSVarianVARIAN UNITY PLUS6002

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameVersionDeveloperClassification
X-PLORBRUNGERrefinement
VARIAN VNMRVNMRstructure solution
Felixstructure solution
X-PLORstructure solution
RefinementMethod: DISTANCE GEOMETRY, RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1
Details: A SET OF FOUR STRUCTURES WERE OBTAINED USING METRIC MATRIX DISTANCE GEOMETRY, AND SUBSEQUENTLY REFINED BY DISTANCE-RESTRAINED MOLECULAR DYNAMICS USING A SET OF INTER-PROTON DISTANCES AND ...Details: A SET OF FOUR STRUCTURES WERE OBTAINED USING METRIC MATRIX DISTANCE GEOMETRY, AND SUBSEQUENTLY REFINED BY DISTANCE-RESTRAINED MOLECULAR DYNAMICS USING A SET OF INTER-PROTON DISTANCES AND DIHEDRAL ANGLE RESTRAINTS DERIVED FROM THE NMR DATA. THE FOUR DISTANCE-REFINED STRUCTURES WERE REFINED FURTHER USING RELAXATION-MATRIX BASED NOE INTENSITY-RESTRAINED MOLECULAR DYNAMICS. ALL CALCULATIONS WERE CARRIED OUT USING THE X-PLOR PROGRAM. THE FINAL FOUR STRUCTURES WERE OBTAINED BY CONJUGATE GRADIENT MINIMIZATION OF THE STRUCTURES OBTAINED BY RELAXATION MATRIX BASED NOE INTENSITY-RESTRAINED MOLECULAR DYNAMICS. THE UNWEIGHTED R(1/6) VALUE WAS USED TO MONITOR THE REFINEMENT. THE R(1/6)-FACTOR IS DEFINED: R(1/6) = SUM{|I(OBS)^(1/6) - K*I(CALC)^(1/6)|} / SUM{I(OBS)^(1/6)}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
NMR ensembleConformer selection criteria: ALL CONFORMERS PRESENTED / Conformers calculated total number: 4 / Conformers submitted total number: 4

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