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Open data
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Basic information
Entry | Database: PDB / ID: 1n4b | ||||||
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Title | Solution Structure of the undecamer CGAAAC*TTTCG | ||||||
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![]() | DNA / interstrand cross-link / alkylated DNA / modified cytosine / alkylated cytosine | ||||||
Function / homology | DNA / DNA (> 10)![]() | ||||||
Method | SOLUTION NMR / distance geometry simulated annealing, molecular dynamics | ||||||
![]() | Webba da Silva, M. / Noronha, A.M. / Noll, D.M. / Miller, P.S. / Colvin, O.M. / Gamcsik, M.P. | ||||||
![]() | ![]() Title: Solution Structure of a DNA Duplex Containing Mispair-Aligned N4C-Ethyl-N4C Interstrand Cross-Linked Cytosines Authors: Webba da Silva, M. / Noronha, A.M. / Noll, D.M. / Miller, P.S. / Colvin, O.M. / Gamcsik, M.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 24.1 KB | Display | ![]() |
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PDB format | ![]() | 16.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 306.8 KB | Display | ![]() |
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Full document | ![]() | 314.9 KB | Display | |
Data in XML | ![]() | 2.7 KB | Display | |
Data in CIF | ![]() | 3.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: DNA chain | Mass: 3333.198 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Interstrand Cross-Linked DNA |
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#2: DNA chain | Mass: 3361.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Interstrand Cross-Linked DNA |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Contents: The synthesis by solid phase methods of DNA duplexes that contain an N4-C-ethyl-N4C interstrand cross-link has been described [Biochemistry,41(2002)760-771]. 2 mM single strand ...Contents: The synthesis by solid phase methods of DNA duplexes that contain an N4-C-ethyl-N4C interstrand cross-link has been described [Biochemistry,41(2002)760-771]. 2 mM single strand concentration in 0.3 mL containing 10 mM sodium phosphate (pH 7.4) and 100 mM NaCl. Solvent system: both 1H2O (95%) and 2H2O (5%), and 99.9 % 2H2O. | |||||||||||||||
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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 / Scattering type: x-ray | ||||||||||||||||||||
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Radiation wavelength | Relative weight: 1 | ||||||||||||||||||||
NMR spectrometer |
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Processing
NMR software | Name: ![]() |
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Refinement | Method: distance geometry simulated annealing, molecular dynamics Software ordinal: 1 Details: A total of 449 restraints were used 243 non-exchangeable 53 exchangeable 44 hydrogen bond 109 dihedral angle |
NMR representative | Selection criteria: closest to the average,lowest energy |
NMR ensemble | Conformer selection criteria: the structure submitted is the lowest energy structure of a an ensemble of selected ten structures Conformers calculated total number: 100 / Conformers submitted total number: 1 |