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Open data
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Basic information
Entry | Database: PDB / ID: 1uhx | ||||||||||||||||||
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Title | Crystal structure of d(GCGAGAGC): the base-intercalated duplex | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / base-intercalated duplex / base-intercalated motif / sheared G:A pair / Deoxyribonucleic acid | Function / homology | COBALT HEXAMMINE(III) / DNA | ![]() Method | ![]() ![]() ![]() ![]() Kondo, J. / Umeda, S.I. / Fujita, K. / Sunami, T. / Takenaka, A. | ![]() ![]() Title: X-ray analyses of d(GCGAXAGC) containing G and T at X: the base-intercalated duplex is still stable even in point mutants at the fifth residue. Authors: Kondo, J. / Umeda, S.I. / Fujita, K. / Sunami, T. / Takenaka, A. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 16.6 KB | Display | ![]() |
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PDB format | ![]() | 9.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 327.3 KB | Display | ![]() |
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Full document | ![]() | 327.3 KB | Display | |
Data in XML | ![]() | 1.3 KB | Display | |
Data in CIF | ![]() | 1.9 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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Unit cell |
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Components on special symmetry positions |
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Components
-DNA chain , 1 types, 1 molecules A
#1: DNA chain | Mass: 2555.539 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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-Non-polymers , 5 types, 73 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/NCO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/NCO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / |
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#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-NA / |
#5: Chemical | ChemComp-NCO / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 36.6 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2-methyl-2,4-pentandiol, hexamine cobalt chloride, magnesium chloride, sodium succinate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→29.2 Å / Num. all: 2142 / Num. obs: 2142 / % possible obs: 100 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 2→2.1 Å / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 2.4 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 29 Å / Num. measured all: 104504 |
Reflection shell | *PLUS % possible obs: 100 % |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: G. PARKINSON ET AL., (1996) ACTACRYST. D52, 57-64
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Displacement parameters |
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Refine analyze | Luzzati coordinate error obs: 0.22 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.19 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å /
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rwork: 0.22 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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