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Yorodumi- PDB-149d: SOLUTION STRUCTURE OF A PYRIMIDINE(DOT)PURINE(DOT) PYRIMIDINE DNA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 149d | ||||||
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Title | SOLUTION STRUCTURE OF A PYRIMIDINE(DOT)PURINE(DOT) PYRIMIDINE DNA TRIPLEX CONTAINING T(DOT)AT, C+(DOT)GC AND G(DOT)TA TRIPLES | ||||||
Components |
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Keywords | DNA / TRIPLEX | ||||||
Function / homology | DNA Function and homology information | ||||||
Method | SOLUTION NMR | ||||||
Authors | Radhakrishnan, I. / Patel, D.J. | ||||||
Citation | Journal: Structure / Year: 1994 Title: Solution structure of a pyrimidine.purine.pyrimidine DNA triplex containing T.AT, C+.GC and G.TA triples. Authors: Radhakrishnan, I. / Patel, D.J. #1: Journal: Biochemistry / Year: 1992 Title: Three-Dimensional Homonuclear Noesy-Tocsy of an Intramolecular Pyrimidine(Dot)Purine(Dot)Pyrimidine DNA Triplex Containing a Central G(Dot)Ta Triple: Nonexchangeable Proton Assignments and Structural Implications Authors: Radhakrishnan, I. / Patel, D.J. / Gao, X. #2: Journal: J.Am.Chem.Soc. / Year: 1992 Title: Solution Conformation of a G(Dot)Ta Triple in an Intramolecular Pyrimidine(Dot)Purine(Dot)Pyrimidine DNA Triplex Authors: Radhakrishnan, I. / Patel, D.J. / Veal, J.M. / Gao, X. #3: Journal: Biochemistry / Year: 1991 Title: NMR Structural Studies of Intramolecular (Y+)N(Dot)(R+)N(Y-)N DNA Triplexes in Solution: Imino and Amino Proton and Nitrogen Markers of G(Dot)Ta Base Triple Formation Authors: Radhakrishnan, I. / Gao, X. / De Los Santos, C. / Live, D. / 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 | 149d.cif.gz | 218.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb149d.ent.gz | 153.1 KB | Display | PDB format |
PDBx/mmJSON format | 149d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 149d_validation.pdf.gz | 310.6 KB | Display | wwPDB validaton report |
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Full document | 149d_full_validation.pdf.gz | 411.8 KB | Display | |
Data in XML | 149d_validation.xml.gz | 31.5 KB | Display | |
Data in CIF | 149d_validation.cif.gz | 47.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/49/149d ftp://data.pdbj.org/pub/pdb/validation_reports/49/149d | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Atom site foot note | 1: THREE RESIDUES IN THE SEQUENCE STUDIED ARE CYTOSINES THAT ARE PROTONATED AT THE N3 POSITION. THESE RESIDUES DIFFER FROM "NORMAL" CYTOSINES IN THAT THEY HAVE A PROTON ATTACHED TO THE N3 NITROGEN. ...1: THREE RESIDUES IN THE SEQUENCE STUDIED ARE CYTOSINES THAT ARE PROTONATED AT THE N3 POSITION. THESE RESIDUES DIFFER FROM "NORMAL" CYTOSINES IN THAT THEY HAVE A PROTON ATTACHED TO THE N3 NITROGEN. IT SHOULD BE NOTED THAT THIS IS NOT A PERMANENT MODIFICATION BUT RATHER A CONSEQUENCE OF THE CONDITIONS UNDER WHICH THE SEQUENCE WAS STUDIED. THESE N3-PROTONATED CYTOSINE RESIDUES HAVE BEEN ASSIGNED THE RESIDUE NAME C IN THE ENTRY AND ATOM H3 HAS BEEN FOOTNOTED. | |||||||||
NMR ensembles |
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-Components
#1: DNA chain | Mass: 2048.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED |
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#2: DNA chain | Mass: 2186.473 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: DNA chain | Mass: 2064.372 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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-Sample preparation
Crystal grow | *PLUS Method: other / Details: NMR |
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-Processing
Software |
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NMR software | Name: X-PLOR / Developer: BRUNGER / Classification: refinement | ||||||||
Refinement | Software ordinal: 1 Details: R VALUE 0.022 RMSD BOND DISTANCES 0.005 ANGSTROMS RMSD BOND ANGLES 2.26 DEGREES | ||||||||
NMR ensemble | Conformers submitted total number: 14 |