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- PDB-1xa2: Cobalt hexammine induced tautomeric shift in Z-DNA: the structure... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1xa2 | ||||||
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Title | Cobalt hexammine induced tautomeric shift in Z-DNA: the structure of d(CGCGCA).d(TGCGCG) in two crystal forms | ||||||
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![]() | DNA / DOUBLE HELIX / Z-DNA | ||||||
Function / homology | COBALT HEXAMMINE(III) / DNA![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Thiyagarajan, S. / Rajan, S.S. / Gautham, N. | ||||||
![]() | ![]() Title: Cobalt hexammine induced tautomeric shift in Z-DNA: the structure of d(CGCGCA)*d(TGCGCG) in two crystal forms. Authors: Thiyagarajan, S. / Rajan, S.S. / Gautham, N. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Structure of d(TGCGCG). d(CGCGCA) in two crystal forms: effects of sequence and crystal packing in Z-DNA Authors: Thiyagarajan, S. / Rajan, S.S. / Gautham, N. | ||||||
History |
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Remark 999 | SEQUENCE This sequence is potentially a left handed Z-DNA forming seqeunce |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 17.3 KB | Display | ![]() |
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PDB format | ![]() | 10.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 389.1 KB | Display | ![]() |
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Full document | ![]() | 392 KB | Display | |
Data in XML | ![]() | 3.7 KB | Display | |
Data in CIF | ![]() | 4.4 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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Unit cell |
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Components
#1: DNA chain | Mass: 1794.206 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 1825.216 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Chemical | ChemComp-NCO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.79 Å3/Da / Density % sol: 30.88 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: MPD, sodium cacodylate, cobalt hexammine chloride, spermine, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 2003 / Details: mirrors |
Radiation | Monochromator: OSMIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→18.11 Å / Num. all: 2766 / Num. obs: 2766 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.63 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 1.71→1.77 Å / Rmerge(I) obs: 0.149 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: standard FIBER MODEL Z-DNA HEXAMER WITH A-T BASE PAIR AT ONE TERMINAL Resolution: 1.71→18.11 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.719 / SU ML: 0.093 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.17 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.745 Å2
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Refinement step | Cycle: LAST / Resolution: 1.71→18.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.71→1.754 Å / Total num. of bins used: 20 /
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