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- PDB-1i34: SOLUTION DNA QUADRUPLEX WITH DOUBLE CHAIN REVERSAL LOOP AND TWO D... -

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Basic information

Entry
Database: PDB / ID: 1i34
TitleSOLUTION DNA QUADRUPLEX WITH DOUBLE CHAIN REVERSAL LOOP AND TWO DIAGONAL LOOPS CONNECTING GGGG TETRADS FLANKED BY G-(T-T) TRIAD AND T-T-T TRIPLE
Components5'-D(*GP*GP*TP*TP*TP*TP*GP*GP*CP*AP*GP*GP*GP*TP*TP*TP*TP*GP*GP*T)-3'
KeywordsDNA / DIAGONAL LOOP / DOUBLE CHAIN REVERSAL LOOP / G(SYN)-G(SYN)-G(ANTI)-G(ANTI) TETRADS / G-(T-T) TRIAD / UNIMOLECULAR G-QUADRUPLEX / T-T-T TRIPLE / DEOXYRIBONUCLEIC ACID
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING, DISTANCE RESTRAINED MOLECULAR DYNAMICS REFINEMENT, RELAXATION MATRIX INTENSITY REFINEMENT
AuthorsKuryavyi, V. / Majumdar, A. / Shallop, A. / Chernichenko, N. / Skripkin, E. / Jones, R. / Patel, D.J.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: A double chain reversal loop and two diagonal loops define the architecture of a unimolecular DNA quadruplex containing a pair of stacked G(syn)-G(syn)-G(anti)-G(anti) tetrads flanked by a G- ...Title: A double chain reversal loop and two diagonal loops define the architecture of a unimolecular DNA quadruplex containing a pair of stacked G(syn)-G(syn)-G(anti)-G(anti) tetrads flanked by a G-(T-T) Triad and a T-T-T triple.
Authors: Kuryavyi, V. / Majumdar, A. / Shallop, A. / Chernichenko, N. / Skripkin, E. / Jones, R. / Patel, D.J.
History
DepositionFeb 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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
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: 5'-D(*GP*GP*TP*TP*TP*TP*GP*GP*CP*AP*GP*GP*GP*TP*TP*TP*TP*GP*GP*T)-3'


Theoretical massNumber of molelcules
Total (without water)6,2581
Polymers6,2581
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)10 / 100STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY, STRUCTURES WITH FAVORABLE NON-BOND ENERGY,STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,BACK-CALCULATED DATA AGREE WITH EXPERIMENTAL NOESY SPECTRUM
RepresentativeModel #3closest to the average, fewest violations

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Components

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


Mass: 6258.019 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
111NOESY
121TOCSY
131DQF-COSY
141COSY-45
151
161
171
181
191
1101
NMR detailsText: SITE-SPECIFIC SUBSTITUTED SAMPLES CONTAINING 8BR-A,8BR-G,DU,5BR-DU, 2,6A, I, 5ME-C ANALOGS AND SITE-SPECIFIC OR UNIFORMLY 13C AND 15N LABELED SAMPLES HAVE BEEN USED

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Sample preparation

Details
Solution-IDContentsSolvent system
15-10 MM DNA (SINGLE STRANDS); 5MM SODIUM PHOSPHATE BUFFER90% H2O/10% D2O
25-10MM DNA (SINGLE STRANDS); 5MM SODIUM PHOSPHATE BUFFER100% D2O
Sample conditionsIonic strength: 150mM NACL / pH: 6.8 / Pressure: 1 atm / Temperature: 278.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian VARIAN UNITY INOVA / Manufacturer: Varian / Model: VARIAN UNITY INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGER, A.T. et al.refinement
VNMR6VARIANcollection
Felix2000MSIprocessing
Insight II2000MSIdata analysis
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING, DISTANCE RESTRAINED MOLECULAR DYNAMICS REFINEMENT, RELAXATION MATRIX INTENSITY REFINEMENT
Software ordinal: 1
Details: A TOTAL OF 100 INITIAL DNA STRUCTURES WERE GENERATED USING THE METRIC MATRIX DISTANCE GEOMETRY PROTOCOL OF X-PLOR WITH THE DISTANCE RESTRAINTS OBTAINED EXPERIMENTALLY SPECIFIED AS NOE. ...Details: A TOTAL OF 100 INITIAL DNA STRUCTURES WERE GENERATED USING THE METRIC MATRIX DISTANCE GEOMETRY PROTOCOL OF X-PLOR WITH THE DISTANCE RESTRAINTS OBTAINED EXPERIMENTALLY SPECIFIED AS NOE. FOURTEEN STRUCTURES WERE IDENTIFIED BASED ON THE CRITERION ACCEPTABLE COVALENT GEOMETRY, LOW DISTANCE RESTRAINT VIOLATIONS AND FAVORABLE NON-BONDED ENERGY. THE VARIATION IN ENERGIES WITHIN THIS SUBSET OF STRUCTURES WAS 46 KCAL/MOL AND WAS SEPARATED FROM THE REMAINING STRUCTURES BY A GAP OF 200 KCAL/MOL. THE TEN BEST STRUCTURES FROM THIS SUBSET OF FOURTEEN WERE FURTHER OPTIMIZED WITH RESTRAINED MOLECULAR DYNAMICS, MOLECULAR MECHANICS AND RELAXATION MATRIX INTENSITY REFINEMENT. THE PROTOCOLS ARE AS FOLLOWS. THE DYNAMICS WAS INITIATED AT 300K AND THE TEMPERATURE WAS INCREASED TO 1000K DURING 7PS. AFTER 0.5 PS THE FORCE CONSTANTS WERE GRADUALLY SCALED DURING 17.5 PSEC IN THE PROPORTION 1: 4: 8 FOR THREE CLASSES OF NOE: EXCHANGEABLE, NONEXCHANGEABLE AND HYDROGEN BONDS, RESP. THE STRUCTURES WERE THEN SLOWLY COOLED TO 300K IN 2.8 PS AND EQUILIBRATED AT 300K FOR 12 PS. SOFT PLANARITY RESTRAINTS WERE SWITCHED OFF BEFORE THE EQUILIBRATION STAGE.THE COORDINATES SAVED EVERY 0.5 PS DURING THE LAST 4.0 PS WERE AVERAGED AND THE AVERAGE STRUCTURE WAS SUBJECTED TO 3000 STEPS OF MINIMIZATION. THE DIHEDRAL ANGLE RESTRAINTS AND HYDROGEN BONDS OF THE GGGG TETRADS WERE MAINTAINED THROUGHOUT. THE OBTAINED STRUCTURES WERE SUBJECTED TO RELAXATION MATRIX INTENSITY REFINEMENT. THE INTENSITY VOLUMES WERE USED AS RESTRAINTS AND NON-EXCHANGEABLE PROTON DISTANCE RESTRAINTS WITH THE SCALE FACTOR OF 0.1 RELATIVE TO THE INTENSITY RESTRAINTS. SOFT PLANARITY RESTRAINTS MAINTAINED DURING RELAXATION REFINEMENTS WERE SWITCHED OFF BEFORE THE FINAL STEPS OF MINIMIZATION. THE RELAXATION PATHWAYS WERE CALCULATED USING CUTOFF 4.5 ANGSTROM AND 7.91 NS ISOTROPIC CORRELATION TIME. THE STRUCTURES EXHIBIT PAIRWISE R.M.S.D. VALUE OF 1.07 A.
NMR representativeSelection criteria: closest to the average, fewest violations
NMR ensembleConformer selection criteria: STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY, STRUCTURES WITH FAVORABLE NON-BOND ENERGY,STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,BACK-CALCULATED DATA AGREE WITH ...Conformer selection criteria: STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY, STRUCTURES WITH FAVORABLE NON-BOND ENERGY,STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,BACK-CALCULATED DATA AGREE WITH EXPERIMENTAL NOESY SPECTRUM
Conformers calculated total number: 100 / Conformers submitted total number: 10

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