+Open data
-Basic information
Entry | Database: PDB / ID: 1fv8 | ||||||||||||||||||
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Title | NMR STUDY OF AN HETEROCHIRAL HAIRPIN | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / Hairpin / heterochiral loop / flexibilty / antisense DNA | Function / homology | DNA / DNA (> 10) | Function and homology information Method | SOLUTION NMR / simulated annealing, torsion angle dynamics | Authors | El Amri, C. / Mauffret, O. / Santamaria, F. / Rayner, B. / Fermandjian, S. | Citation | Journal: J.Biomol.Struct.Dyn. / Year: 2001 | Title: NMR study of a heterochiral DNA hairpin:impact of L-enantiomery in the loop. Authors: El Amri, C. / Mauffret, O. / Santamariar, F. / Tevanian, G. / Rayner, B. / Fermandjian, S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fv8.cif.gz | 72.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fv8.ent.gz | 55.4 KB | Display | PDB format |
PDBx/mmJSON format | 1fv8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fv8_validation.pdf.gz | 304.7 KB | Display | wwPDB validaton report |
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Full document | 1fv8_full_validation.pdf.gz | 350.7 KB | Display | |
Data in XML | 1fv8_validation.xml.gz | 3.9 KB | Display | |
Data in CIF | 1fv8_validation.cif.gz | 5.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fv/1fv8 ftp://data.pdbj.org/pub/pdb/validation_reports/fv/1fv8 | 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: 3332.210 Da / Num. of mol.: 1 / Fragment: AT(L)C HAIRPIN / Source method: obtained synthetically Details: This sequence comes from a pBR322 topoisomerase II cleavage site |
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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 structure was determined using standard 2D homonuclear techniques, and PFG to measure the diffusion constant |
-Sample preparation
Details |
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Sample conditions | Ionic strength: 0.025 / pH: 6 / Temperature: 293 K | |||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 500 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing, torsion angle dynamics / Software ordinal: 1 Details: The structures are based on a total of 252 restraints, distance constraints, 56 dihedral angle restraints,9 distance restraints from hydrogen bonds, and 4 planarity constraints. The ...Details: The structures are based on a total of 252 restraints, distance constraints, 56 dihedral angle restraints,9 distance restraints from hydrogen bonds, and 4 planarity constraints. The calculations were performed on the 11 central residues. | ||||||||||||||||||||
NMR representative | Selection criteria: closest to the average,minimized average structure | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 11 |