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Yorodumi- PDB-136d: SOLUTION STRUCTURE OF A PURINE(DOT)PURINE(DOT)PYRIMIDINE DNA TRIP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 136d | ||||||
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Title | SOLUTION STRUCTURE OF A PURINE(DOT)PURINE(DOT)PYRIMIDINE DNA TRIPLEX CONTAINING G(DOT)GC AND T(DOT)AT TRIPLES | ||||||
Components | DNA TRIPLEX | ||||||
Keywords | DNA / TRIPLEX | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / RESTRAINED MOLECULAR DYNAMICS, DISTANCE GEOMETRY | ||||||
Authors | Radhakrishnan, I. / Patel, D.J. | ||||||
Citation | Journal: Structure / Year: 1993 Title: Solution structure of a purine.purine.pyrimidine DNA triplex containing G.GC and T.AT triples. Authors: Radhakrishnan, I. / Patel, D.J. #1: Journal: J.Am.Chem.Soc. / Year: 1993 Title: Solution Structure of an Intramolecular Purine(Dot)Purine(Dot)Pyrimidine DNA Triplex Authors: Radhakrishnan, I. / Patel, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 136d.cif.gz | 261.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb136d.ent.gz | 181.9 KB | Display | PDB format |
PDBx/mmJSON format | 136d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 136d_validation.pdf.gz | 309.1 KB | Display | wwPDB validaton report |
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Full document | 136d_full_validation.pdf.gz | 514.1 KB | Display | |
Data in XML | 136d_validation.xml.gz | 46.4 KB | Display | |
Data in CIF | 136d_validation.cif.gz | 60.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/36/136d ftp://data.pdbj.org/pub/pdb/validation_reports/36/136d | HTTPS FTP |
-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: 9552.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR details | Text: STRUCTURE ANALYSES WERE CONDUCTED ON SIXTEEN STRUCTURES INCLUDING FOURTEEN STRUCTURES TAKEN FROM THE RESTRAINED MOLECULAR DYNAMICS TRAJECTORIES OF THE TWO REFINEMENTS, AND THE TWO AVERAGED ...Text: STRUCTURE ANALYSES WERE CONDUCTED ON SIXTEEN STRUCTURES INCLUDING FOURTEEN STRUCTURES TAKEN FROM THE RESTRAINED MOLECULAR DYNAMICS TRAJECTORIES OF THE TWO REFINEMENTS, AND THE TWO AVERAGED MINIMIZED STRUCTURES. THE COORDINATES FOR THE TWO AVERAGED MINIMIZED STRUCTURES CAN BE FOUND IN PROTEIN DATA BANK ENTRIES 134D AND 135D, RESPECTIVELY. THE COORDINATES FOR THE 14 STRUCTURES FROM THE RESTRAINED MOLECULAR DYNAMICS TRAJECTORIES CAN BE FOUND IN ENTRY 136D. |
-Processing
Software |
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NMR software | Name: X-PLOR / Developer: BRUNGER / Classification: refinement | |||||||||
Refinement | Method: RESTRAINED MOLECULAR DYNAMICS, DISTANCE GEOMETRY / Software ordinal: 1 Details: RESTRAINED MOLECULAR DYNAMICS CALCULATIONS WERE DONE ON IDEALIZED A'- AND B-FORM STARTING STRUCTURES. ONLY THE TRIPLEX REGION AND THE FIRST AND LAST RESIDUES OF EACH OF THE TWO LOOPS IN THE ...Details: RESTRAINED MOLECULAR DYNAMICS CALCULATIONS WERE DONE ON IDEALIZED A'- AND B-FORM STARTING STRUCTURES. ONLY THE TRIPLEX REGION AND THE FIRST AND LAST RESIDUES OF EACH OF THE TWO LOOPS IN THE SEQUENCE WERE CONSIDERED. THE REFINEMENT WAS CONDUCTED IN TWO STAGES. IN THE FIRST STAGE, SIX STRUCTURES WERE CALCULATED (THREE FROM EACH STARTING STRUCTURE) USING DISTANCE RESTRAINTS. IN THE SECOND STAGE, TWO OF THE SIX STRUCTURES WERE REFINED DIRECTLY AGAINST PRIMARY NOE DATA. THE R(1/6) VALUE WAS USED TO MONITOR THE REFINEMENT DURING THIS STAGE. THE FINAL R(1/6) VALUES FOR THE TWO AVERAGED MINIMIZED STRUCTURES WERE 0.04 AND 0.045. THE SUMMATION RUNS THROUGH ALL OBSERVED, QUANTIFIABLE CROSSPEAK INTENSITIES IN NOESY SPECTRA RECORDED AT MIXING TIMES OF 40, 90 AND 150 MS. RMSD BOND DISTANCES 0.016 ANGSTROMS RMSD BOND ANGLES 3.96 DEGREES RMS DEVIATIONS FROM IDEALIZED GEOMETRY FOR THE TWO AVERAGED MINIMIZED STRUCTURES ARE AS FOLLOWS: | |||||||||
NMR ensemble | Conformers submitted total number: 14 | |||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | |||||||||
Refine LS restraints | *PLUS
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