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- PDB-1c32: SOLUTION STRUCTURE OF A QUADRUPLEX FORMING DNA AND ITS INTERMIDIATE -

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Basic information

Entry
Database: PDB / ID: 1c32
TitleSOLUTION STRUCTURE OF A QUADRUPLEX FORMING DNA AND ITS INTERMIDIATE
ComponentsDNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3')
KeywordsDNA / APTAMER / QUADRUPLEX / METAL BINDING DNA / POTASSIUM / THROMBIN
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / STRUCTURE REFINEMENT OF THE DNA WAS PERFORMED USING COMPLETE RELAXATION MATRIX, RESTRAINED MOLECULAR DYNAMICS.
AuthorsBolton, P.H. / Marathias, V.M. / Wang, K.
Citation
Journal: Nucleic Acids Res. / Year: 2000
Title: Structures of the potassium-saturated, 2:1, and intermediate, 1:1, forms of a quadruplex DNA.
Authors: Marathias, V.M. / Bolton, P.H.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: Determination of the Number and Location of the Manganese Binding Sites of DNA Quadruplexes in Solution by EPR and NMR in the Presence and Absence of Thrombin
Authors: Bolton, P.H. / Marathias, V.M. / Wang, K.
History
DepositionJul 24, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,7431
Polymers4,7431
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 / 1080-88 AND 91-100 PS STRUCTURES FORM TRAJECTORY
RepresentativeModel #10100ps structure

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Components

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


Mass: 4743.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THROMBIN BINDING QUADRUPLEX

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121PE-COSY
131ROESY
141BASD-TOCSY
152WATERGATED NOESY
NMR detailsText: THIS FILE CONTAINS THE COORDINATES OF 10 STRUCTURES FROM 80-88 AND 91-100 PS.

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Sample preparation

Details
Solution-IDContents
1140 MM NACL, 5 MM KCL, 20 MM TRISD11, PH=7.0 BUFFER
2140 MM NACL, 5 MM KCL, 20 MM TRISD11, PH=7.0 BUFFER
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1140 mM NACL 71 atm15 K
2140 mM NACL 71 atm5 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian UNITYPLUSVarianUNITYPLUS4002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1BVARIANcollection
VNMR6.1BVARIANprocessing
Felix970MSIprocessing
Felix970MSIrefinement
X-PLOR3.1BRUNGERstructure solution
X-PLOR3.1BRUNGERrefinement
RefinementMethod: STRUCTURE REFINEMENT OF THE DNA WAS PERFORMED USING COMPLETE RELAXATION MATRIX, RESTRAINED MOLECULAR DYNAMICS.
Software ordinal: 1
Details: 303 NOE VOLUME CONSTRAINTS FROM THE 100 MS AND 498 NOE FROM THE 250 MS NOESY DATA WERE USED. IN ADDITION 10 NOE CONSTRAINTS INVOLVING THE IMINO PROTONS OF RESIDUES G1, G5, G6, G8, G10, G14, ...Details: 303 NOE VOLUME CONSTRAINTS FROM THE 100 MS AND 498 NOE FROM THE 250 MS NOESY DATA WERE USED. IN ADDITION 10 NOE CONSTRAINTS INVOLVING THE IMINO PROTONS OF RESIDUES G1, G5, G6, G8, G10, G14, AND G15 WERE USED AS DISTANCE CONSTRAINTS. FOUR HYDROGEN BONDS WERE USED FOR EACH GUANINE INVOLVED IN A QUARTET. EXPERIMENTAL COUPLING CONSTANTS WERE USED TO GENERATE 45 DIHEDRAL CONSTRAINTS, 15 FROM BASHD-TOCSY EXPERIMENTS (H3*-31P), AND 30 FROM PE-COSY DATA (H1*-C1*- C2*-1H2* AND H1*-C1*-C2*-2H2*). ADDITIONAL CONSTRAINTS WERE USED TO KEEP THE PURINE RINGS PLANAR. THE STARTING STRUCTURE USED WAS THE STRUCTURE OBTAINED IN A PREVIOUS REFINEMENT. THE NON-BONDED INTERACTION CUT-OFF WAS SET TO 11.5 A, USING X-PLOR PROTOCOLS. THE ACTIVE DISTANCE OF THE SWITCHING FUNCTIONS WAS 7.5 TO 10.5 A. THE DISTANCE CUT-OFF FOR THE HYDROGEN BONDING INTERACTIONS WAS 7.5 A. THE SWITCHING FUNCTION FOR HYDROGEN BONDING INTERACTIONS WAS ACTIVE FROM 4.0 TO 6.5 A. THE ENERGY OF THE STARTING STRUCTURE WAS MINIMIZED IN 200 STEPS OF POWELL'S CONJUGATE GRADIENT MINIMIZATION. THE RELAXATION MATRIX REFINEMENTS WERE CARRIED OUT IN VACUUM AT 300K WITH A RELATIVE WEIGHTING OF ALL THE EXPERIMENTAL CONSTRAINTS (NOE, DISTANCE AND DIHEDRAL) OF 60 KCAL/MOL. SUBSEQUENTLY, A 100 PS RELAXATION MATRIX TRAJECTORY WAS CONDUCTED WITH STRUCTURES SAVED EVERY 2 PS. THE TRAJECTORIES STABILIZED AFTER 30 PS. UPON COMPLETION OF THE SIMULATION AN ADDITIONAL 200 STEP CONJUGATE GRADIENT MINIMIZATION WAS CONDUCTED TO PRODUCE THE FINAL STRUCTURES. THE ROOT MEAN SQUARE DEVIATION {OF WHAT?} WAS CALCULATED TO BE 0.14. THE NOE CROSS-PEAK VOLUMES OF THE STRUCTURES OBTAINED BETWEEN 80-100 PS AT INTERVALS OF 2 PS WERE BACKCALCULATED USING THE FELIX 970 SOFTWARE PACKAGE (MSI INC.) PARAMETERS USED IN THE BACKCALCULATION PROTOCOL ARE AS FOLLOWS: A CORRELATION TIME OF 5.0 NS, A Z-LEAKAGE RATE OF 3.0 S-1 AND A DISTANCE CUT OFF OF 7.5 A. NOE SPECTRA OF THESE 10 STRUCTURES WERE THEN BACKCALCULATED AND AVERAGED. 40 NOE INTENSITIES FROM THE EXPERIMENTAL NOESY SPECTRA WERE USED TO NORMALIZE THE BACKCALCULATED TO THE THEORETICAL NOES. THE NORMALIZATION AND AVERAGING PROCESSES WERE CONDUCTED ON A IN HOUSE PROGRAM. THE RMS, R AND Q VALUES OF THE AVERAGED STRUCTURE THAT ARE 0.28, 0.68 AND 0.30.
NMR representativeSelection criteria: 100ps structure
NMR ensembleConformer selection criteria: 80-88 AND 91-100 PS STRUCTURES FORM TRAJECTORY
Conformers calculated total number: 10 / Conformers submitted total number: 10

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