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Yorodumi- PDB-1c32: SOLUTION STRUCTURE OF A QUADRUPLEX FORMING DNA AND ITS INTERMIDIATE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c32 | ||||||||||||||||||
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Title | SOLUTION STRUCTURE OF A QUADRUPLEX FORMING DNA AND ITS INTERMIDIATE | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / APTAMER / QUADRUPLEX / METAL BINDING DNA / POTASSIUM / THROMBIN | Function / homology | DNA / DNA (> 10) | Function and homology information Method | SOLUTION NMR / STRUCTURE REFINEMENT OF THE DNA WAS PERFORMED USING COMPLETE RELAXATION MATRIX, RESTRAINED MOLECULAR DYNAMICS. | Authors | Bolton, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c32.cif.gz | 115.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c32.ent.gz | 88.3 KB | Display | PDB format |
PDBx/mmJSON format | 1c32.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/1c32 ftp://data.pdbj.org/pub/pdb/validation_reports/c3/1c32 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 4743.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THROMBIN BINDING QUADRUPLEX |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: THIS FILE CONTAINS THE COORDINATES OF 10 STRUCTURES FROM 80-88 AND 91-100 PS. |
-Sample preparation
Details |
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Sample conditions |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: 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 representative | Selection criteria: 100ps structure | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: 80-88 AND 91-100 PS STRUCTURES FORM TRAJECTORY Conformers calculated total number: 10 / Conformers submitted total number: 10 |