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Open data
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Basic information
Entry | Database: PDB / ID: 1p24 | ||||||||||||||||||
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Title | Crystal structure of cobalt(II)-d(GGCGCC)2 | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / B-DNA / cobalt binding | Function / homology | : / DNA | ![]() Method | ![]() ![]() ![]() ![]() Labiuk, S.L. / Delbaere, L.T. / Lee, J.S. | ![]() ![]() Title: Cobalt(II), nickel(II) and zinc(II) do not bind to intra-helical N(7) guanine positions in the B-form crystal structure of d(GGCGCC) Authors: Labiuk, S.L. / Delbaere, L.T. / Lee, J.S. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 26.3 KB | Display | ![]() |
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PDB format | ![]() | 16.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 383.4 KB | Display | ![]() |
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Full document | ![]() | 395.2 KB | Display | |
Data in XML | ![]() | 4.7 KB | Display | |
Data in CIF | ![]() | 5.9 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 1810.205 Da / Num. of mol.: 5 / Source method: obtained synthetically / Details: Synthesized by AlphaDNA (Quebec, PQ, Canada) #2: Chemical | ChemComp-CO / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.72 Å3/Da / Density % sol: 66.7 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.1 Details: DNA, Taps-HCl, CoCl2, glycerol, MPD, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 10, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5088 Å / Relative weight: 1 |
Reflection | Resolution: 3.02→43 Å / Num. all: 2731 / Num. obs: 2731 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 20.8 Å2 / Rsym value: 0.11 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 3.02→3.15 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.51 / % possible all: 69.9 |
Reflection | *PLUS Highest resolution: 3 Å / Num. measured all: 138163 / Rmerge(I) obs: 0.11 |
Reflection shell | *PLUS % possible obs: 69.9 % / Rmerge(I) obs: 0.51 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: NDB ENTRY BD0040 Resolution: 3.02→15 Å / Isotropic thermal model: grouped B values / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 37.9 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.02→15 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 3 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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