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Yorodumi- PDB-1juu: NMR Structure of a Parallel Stranded DNA Duplex at Atomic Resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 1juu | ||||||
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Title | NMR Structure of a Parallel Stranded DNA Duplex at Atomic Resolution | ||||||
Components |
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Keywords | DNA / Parallel stranded / DNA duplex | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / simulated annealing, molecular dynamics | ||||||
Authors | Parvathy, V.R. / Bhaumik, S.R. / Chary, K.V.R. / Govil, G. / Liu, K. / Howard, F.B. / Miles, H.T. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2002 Title: NMR structure of a parallel-stranded DNA duplex at atomic resolution. Authors: Parvathy, V.R. / Bhaumik, S.R. / Chary, K.V. / Govil, G. / Liu, K. / Howard, F.B. / Miles, H.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1juu.cif.gz | 299.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1juu.ent.gz | 245 KB | Display | PDB format |
PDBx/mmJSON format | 1juu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1juu_validation.pdf.gz | 314.3 KB | Display | wwPDB validaton report |
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Full document | 1juu_full_validation.pdf.gz | 453.9 KB | Display | |
Data in XML | 1juu_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 1juu_validation.cif.gz | 27.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ju/1juu ftp://data.pdbj.org/pub/pdb/validation_reports/ju/1juu | 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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NMR ensembles |
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-Components
#1: DNA chain | Mass: 3581.368 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The DNA duplex was Synthesized with an Applied Biosystems Model 380B DNA synthesizer using solid state phosphoramidate chemistry |
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#2: DNA chain | Mass: 3581.368 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: COSY, NOESY, TOCSY |
NMR details | Text: Structure was determined using 2D homonuclear experiments. |
-Sample preparation
Details | Contents: 5 mM concentration of each dodecamer strand, 0.05 M deuterated sodium acetate buffer and 0.1 M NaCl Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 100mM NaCl / pH: 5.5 / Pressure: ambient / Temperature: 303 K |
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 | Type: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Method: simulated annealing, molecular dynamics / Software ordinal: 1 Details: Structure was calculated using 78 nOe constraints, 28 hydrogen bond constraints, and 162 dihedral angle constraints. | ||||||||||||
NMR representative | Selection criteria: fewest violations,lowest energy | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |