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Open data
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Basic information
Entry | Database: PDB / ID: 1ndn | ||||||
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Title | MOLECULAR STRUCTURE OF NICKED DNA. MODEL T4 | ||||||
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![]() | DNA / B-DNA / DOUBLE HELIX / NICKED | ||||||
Function / homology | DNA / DNA (> 10)![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Aymani, J. / Coll, M. / Van Der Marel, G.A. / Van Boom, J.H. / Wang, A.H.-J. / Rich, A. | ||||||
![]() | ![]() Title: Molecular structure of nicked DNA: a substrate for DNA repair enzymes. Authors: Aymami, J. / Coll, M. / van der Marel, G.A. / van Boom, J.H. / Wang, A.H. / Rich, A. #1: ![]() Title: Molecular Structure of the Netropsin-d(CGCGATATCGCG) Complex. DNA Conformation in an Alternating AT Segment Authors: Coll, M. / Aymami, J. / Van Der Marel, G.A. / Van Boom, J.H. / Rich, A. / Wang, A.H.-J. #2: ![]() Title: A Bifurcated Hydrogen-Bonded Conformation in the d(*A(dot)*T) Base Pairs of the DNA Dodecamer d(CGCAAATTTGCG) and Its Complex With Distamycin Authors: Coll, M. / Frederick, C.A. / Wang, A.H.-J. / Rich, A. #3: ![]() Title: Crystal Structure Analysis of a Complete Turn of B-DNA Authors: Wing, R. / Drew, H. / Takano, T. / Broka, C. / Tanaka, S. / Itakura, K. / Dickerson, R.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 23.3 KB | Display | ![]() |
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PDB format | ![]() | 13.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 324.6 KB | Display | ![]() |
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Full document | ![]() | 348.9 KB | Display | |
Data in XML | ![]() | 4.6 KB | Display | |
Data in CIF | ![]() | 6.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: DNA chain | Mass: 3681.420 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 1800.203 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: DNA chain | Mass: 1800.203 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.01 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 5 / Details: pH 5.00, VAPOR DIFFUSION, temperature 277.00K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 5 / Method: unknown | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU AFC-5R / Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 3 Å / Num. obs: 553 / Observed criterion σ(F): 2 |
Reflection | *PLUS Highest resolution: 3 Å / Observed criterion σ(F): 2 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refine Biso |
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Refinement step | Cycle: LAST / Highest resolution: 3 Å
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