+Open data
-Basic information
Entry | Database: PDB / ID: 1jrv | ||||||
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Title | SOLUTION STRUCTURE OF DAATAA DNA BULGE | ||||||
Components |
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Keywords | DNA / DNA BULGE / FIVE-NUCLEOTIDE BULGE LOOP / DEOXYRIBONUCLEIC ACID | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / matrix relaxation (MARDIGRAS); torsion angle dynamics (DYANA); ENERGY MINIMIZATION (AMBER) | ||||||
Authors | Gollmick, F.A. / Lorenz, M. / Dornberger, U. / von Langen, J. / Diekmann, S. / Fritzsche, H. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2002 Title: Solution structure of dAATAA and dAAUAA DNA bulges. Authors: Gollmick, F.A. / Lorenz, M. / Dornberger, U. / von Langen, J. / Diekmann, S. / Fritzsche, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jrv.cif.gz | 272.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jrv.ent.gz | 222.7 KB | Display | PDB format |
PDBx/mmJSON format | 1jrv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jrv_validation.pdf.gz | 321.1 KB | Display | wwPDB validaton report |
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Full document | 1jrv_full_validation.pdf.gz | 461.9 KB | Display | |
Data in XML | 1jrv_validation.xml.gz | 5.7 KB | Display | |
Data in CIF | 1jrv_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/1jrv ftp://data.pdbj.org/pub/pdb/validation_reports/jr/1jrv | 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: 5220.412 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3663.392 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using standard 2D homonuclear and heteronuclear techniques |
-Sample preparation
Details |
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Sample conditions |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | ||||||||||||||||||||
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Radiation wavelength | Relative weight: 1 | ||||||||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: matrix relaxation (MARDIGRAS); torsion angle dynamics (DYANA); ENERGY MINIMIZATION (AMBER) Software ordinal: 1 Details: the structures are based on a total of 906 restraints, 645 are NOE-derived distance constraints, 235 dihedral angle restraints, 26 distance restraints from hydrogen bonds. | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 400 / Conformers submitted total number: 15 |