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- PDB-2a5p: Monomeric parallel-stranded DNA tetraplex with snap-back 3+1 3' G... -

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Basic information

Entry
Database: PDB / ID: 2a5p
TitleMonomeric parallel-stranded DNA tetraplex with snap-back 3+1 3' G-tetrad, single-residue chain reversal loops, GAG triad in the context of GAAG diagonal loop, NMR, 8 struct.
Components5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*IP*GP*AP*GP*GP*GP*TP*GP*GP*GP*GP*AP*AP*GP*G)-3'
KeywordsDNA / MONOMERIC PARALLEL-STRANDED QUADRUPLEX / C-MYC PROMOTER 3+1 G-TETRAD / SINGLE NUCLEOTIDE CHAIN REVERSAL LOOP / GAG TRIAD / GAAG LOOP
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING, DISTANCE RESTRAINED MOLECULAR DYNAMICS REFINEMENT, RELAXATION MATRIX INTENSITY REFINEMENT
AuthorsPhan, A.T. / Kuryavyi, V.V. / Gaw, H.Y. / Patel, D.J.
CitationJournal: Nat.Chem.Biol. / Year: 2005
Title: Small-molecule interaction with a five-guanine-tract G-quadruplex structure from the human MYC promoter.
Authors: Phan, A.T. / Kuryavyi, V. / Gaw, H.Y. / Patel, D.J.
History
DepositionJun 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*IP*GP*AP*GP*GP*GP*TP*GP*GP*GP*GP*AP*AP*GP*G)-3'


Theoretical massNumber of molelcules
Total (without water)7,7021
Polymers7,7021
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)8 / 100back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1lowest energy

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Components

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


Mass: 7701.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: c-MYC gene / Source: (natural) Homo sapiens (human)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111H-1H NOESY
1211H-1H TOCSY
1311H-31P COSY
1411H-1H COSY
1511H-15N JRHMQC
1611H-15N HMBC
1711H-13C JRHM 1H-13C HMBC
1811H-13C HSQC
1911H-13C sHMBC
11011H-31P TOCSY
NMR detailsText: A TOTAL OF 100 INITIAL DNA STRUCTURES WERE GENERATED USING THE METRIC MATRIX DISTANCE GEOMETRY PROTOCOL WITH THE EXPERIMENTAL DISTANCE RESTRAINTS SPECIFIED WITH THE R-6 AVERAGING OPTION. EIGHT ...Text: A TOTAL OF 100 INITIAL DNA STRUCTURES WERE GENERATED USING THE METRIC MATRIX DISTANCE GEOMETRY PROTOCOL WITH THE EXPERIMENTAL DISTANCE RESTRAINTS SPECIFIED WITH THE R-6 AVERAGING OPTION. EIGHT BEST STRUCTURES SELECTED ON THE BASIS OF GOOD COVALENT GEOMETRY, LOW DISTANCE RESTRAINT VIOLATION AND FAVOURABLE NON-BONDED ENERGY TERMS 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 14 PS AND EQUILIBRATED AT 300K FOR 12 PS. THE COORDINATES SAVED EVERY 0.5 PS DURING THE LAST 4.0 PS WERE AVERAGED AND THE AVERAGE STRUCTURE WAS SUBJECTED TO MINIMIZATION UNTIL THE GRADIENT OF ENERGY WAS LESS THAN 0.1KCAL/MOL. SOFT PLANARITY RESTRAINTS IMPOSED ON TETRADS AND TRIAD BEFORE HEATING WERE EXCLUDED AT THE EQUILIBRATION STAGE. THE DIHEDRAL AND HYDROGEN-BONDING RESTRAINTS FOR TETRADS, WERE MAINTAINED THROUGHOUT. ALL EIGHT STRUCTURES WERE SUBJECTED TO RELAXATION MATRIX INTENSITY REFINEMENT. THE INTENSITY VOLUMES OF NON-EXCHANGEABLE PROTONS WERE USED AS RESTRAINTS WITH EXCHANGEABLE PROTONS REPLACED BY DEUTERONS. DYNAMICS STARTED AT 5K AND THE SYSTEM WAS HEATHED UP TO 300 K IN 0.6 PSEC. THE FORCE CONSTANT FOR NOE INTENSITIES WAS GRADUALLY INCREASED FROM 0 TO 400 KCAL*MOL-1*A-2 WITH SIMULTANEOUS DECREASE OF THE DISTANCE FORCE CONSTANTS FOR NON-EXCHANGEABLE PROTONS FROM 32 to 16. AFTER EQUILIBRATION AT 300 K FOR 3 PSEC THE RESULTING STRUCTURES WERE SUBJECTED TO MINIMIZATION UNTIL THE GRADIENT OF ENERGY WAS LESS THAN 0.1KCAL/MOL. THE DISTANCE RESTRAINTS FOR EXCHANGEABLE PROTONS HYDROGEN BONDS AND DIHEDRAL ANGLE RESTRAINTS WERE MAINTAINED. SOFT PLANARITY RESTRAINTS WEERE SET FOR TETRAD (1 KCAL*MOL-1*A-2) AND TRIAD (0.5 KCAL*MOL-1*A-2).

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Sample preparation

Details
Solution-IDContentsSolvent system
170 MM KCL 20 MM POTASSIUM PHOSPHATE, 90% H2O, 10% D2O90% H2O/10% D2O
270 MM KCL 20 MM POTASSIUM PHOSPHATE, 100% D2O100% D2O
Sample conditionsIonic strength: 90 mM / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VARIAN UNITY INOVAVarianVARIAN UNITY INOVA6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
XPLOR3.851AT BRUNGERrefinement
VNMR6VARIANcollection
Felix2000ACCELRYSprocessing
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING, DISTANCE RESTRAINED MOLECULAR DYNAMICS REFINEMENT, RELAXATION MATRIX INTENSITY REFINEMENT
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 100 / Conformers submitted total number: 8

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