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Open data
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Basic information
Entry | Database: PDB / ID: 1dno | ||||||||||||||||||
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Title | A-DNA/RNA DODECAMER R(GCG)D(TATACGC) MG BINDING SITES | ||||||||||||||||||
![]() | DNA/RNA (5'-R(*![]() DNA-RNA HYBRID / DNA CONFORMATION / RNA/DNA HYBRID / METAL IONS / DNA-RNA COMPLEX / DNA-RNA HYBRID COMPLEX | Function / homology | DNA/RNA hybrid | ![]() Method | ![]() ![]() ![]() ![]() Robinson, H. / Gao, Y.-G. / Sanishvili, R. / Joachimiak, A. / Wang, A.H.-J. | ![]() ![]() Title: Hexahydrated magnesium ions bind in the deep major groove and at the outer mouth of A-form nucleic acid duplexes. Authors: Robinson, H. / Gao, Y.G. / Sanishvili, R. / Joachimiak, A. / Wang, A.H. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 25.7 KB | Display | ![]() |
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PDB format | ![]() | 15.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 368.3 KB | Display | ![]() |
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Full document | ![]() | 372 KB | Display | |
Data in XML | ![]() | 4.8 KB | Display | |
Data in CIF | ![]() | 6.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1dntC ![]() 1dnxC ![]() 1dnzC C: citing same article ( |
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Similar structure data | |
Other databases |
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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/RNA hybrid | Mass: 3093.005 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-MG / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 2-MPD, CACODYLATE, SPERMINE, MGCL2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Nov 16, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03321 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→20 Å / Num. all: 10433 / Num. obs: 10433 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 37.3 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 11 % / Rmerge(I) obs: 0.092 / Mean I/σ(I) obs: 23.8 / % possible all: 91.7 |
Reflection | *PLUS Redundancy: 12.1 % |
Reflection shell | *PLUS Rmerge(I) obs: 0.18 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: NDB ID ADJ043 Resolution: 1.4→20 Å / Num. parameters: 2139 / Num. restraintsaints: 1830 / Cross valid method: A POSTERIORI / σ(F): 0 / σ(I): 0 / Stereochemistry target values: G.PARKINSON ET AL.
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Solvent computation | Solvent model: SHELXL SWAT OPTION | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 534 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % / Num. reflection all: 10217 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_plane_restr / Dev ideal: 0.07 |