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Open data
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Basic information
Entry | Database: PDB / ID: 1jes | ||||||||||||||||||
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Title | Crystal Structure of a Copper-Mediated Base Pair in DNA | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / Cu / copper / Z-DNA / dodecamer / duplex / unnatural / designed | Function / homology | COPPER (II) ION / DNA / DNA (> 10) | ![]() Method | ![]() ![]() ![]() ![]() Atwell, S. / Meggers, E. / Spraggon, G. / Schultz, P.G. | ![]() ![]() Title: Structure of a Copper-Mediated Base Pair in DNA Authors: Atwell, S. / Meggers, E. / Spraggon, G. / Schultz, P.G. #1: ![]() Title: A Novel Copper-Mediated DNA Base Pair Authors: Meggers, E. / Holland, P.L. / Tolman, W.B. / Romesberg, F.E. / Schultz, P.G. #2: ![]() Title: Left-handed double helical DNA: variations in the backbone conformation Authors: Wang, A.G.-J. / Quigley, G.J. / Kolpak, F.J. / van Der Marel, G. / van Boom, J.H. / Rich, A. #3: ![]() Title: Structure of a B-DNA dodecamer: conformation and dynamics Authors: Drew, H.R. / Wing, R.M. / 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 | ![]() | 25.9 KB | Display | ![]() |
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PDB format | ![]() | 17.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 387.2 KB | Display | ![]() |
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Full document | ![]() | 388.7 KB | Display | |
Data in XML | ![]() | 4.6 KB | Display | |
Data in CIF | ![]() | 6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 3648.371 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da / Density % sol: 32.43 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10% MPD, 40 mM Na Cacodylate, 12 mM Spermine tetra-HCl, 80 mM NaCl, 20 mM MgCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 140 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 6, 2001 / Details: Curved Si (111) | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.5→50 Å / Num. all: 47272 / Num. obs: 47190 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 14.058 Å2 / Rsym value: 0.096 / Net I/σ(I): 46.7 | ||||||||||||
Reflection shell | Resolution: 1.49→1.54 Å / Rmerge(I) obs: 0.686 / % possible all: 84.1 | ||||||||||||
Reflection | *PLUS Num. obs: 8531 / Num. measured all: 47272 / Rmerge(I) obs: 0.096 | ||||||||||||
Reflection shell | *PLUS % possible obs: 84.1 % / Rmerge(I) obs: 0.686 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: initial map fit with mononucleotides Resolution: 1.5→50 Å / Cross valid method: free r / σ(F): 0 / σ(I): 0 Stereochemistry target values: G. Parkinson, J. Vojtechovsky, L. Clowney, A.T. Brunger, H.M. Berman, New Parameters for the Refinement of Nucleic Acid Containing Structures, Acta Cryst. D, 52, 57-64 (1996). Details: The fofc maps indicated an alternate conformation for the phosphate of B23, and so the structure was refined with two conformations for the phosphate of B23 (excepting the O5') and most of ...Details: The fofc maps indicated an alternate conformation for the phosphate of B23, and so the structure was refined with two conformations for the phosphate of B23 (excepting the O5') and most of residue B22 (excepting O5'), each with 0.5 occupancy.
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.5→50 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 50 Å / Num. reflection obs: 8531 / σ(F): 0 / % reflection Rfree: 8 % / Rfactor obs: 0.169 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |