+Open data
-Basic information
Entry | Database: PDB / ID: 1ue2 | ||||||||||||||||||
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Title | Crystal structure of d(GC38GAAAGCT) | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / base-intercalated duplex / mini-hairpin structure / sheared G:A pair / zipper-like duplex | Function / homology | COBALT HEXAMMINE(III) / DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / HEAVY-ATOM METHOD / Resolution: 1.4 Å | Authors | Sunami, T. / Kondo, J. / Hirao, I. / Watanaba, K. / Miura, K. / Takenaka, A. | Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 | Title: Structure of d(GCGAAAGC) (hexagonal form): a base-intercalated duplex as a stable structure. Authors: Sunami, T. / Kondo, J. / Hirao, I. / Watanabe, K. / Miura, K.I. / Takenaka, A. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ue2.cif.gz | 16.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ue2.ent.gz | 10.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ue2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ue/1ue2 ftp://data.pdbj.org/pub/pdb/validation_reports/ue/1ue2 | HTTPS FTP |
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-Related structure data
-Links
-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
#1: DNA chain | Mass: 2890.734 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-NCO / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 31.48 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 2,6-diaminopyridine, magnesium chloride, sodium chloride, hexaamminecobalt(III) chloride, 2-methyl-2,4-pentanediol, MEGA-10, sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 293 K / 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: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 18, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→18 Å / Num. all: 5562 / Num. obs: 5553 / % possible obs: 99.9 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 1.4→1.43 Å / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 2.6 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 546817 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: HEAVY-ATOM METHOD / Resolution: 1.4→10 Å / σ(F): 3 Stereochemistry target values: G. PARKINSON ET AL., (1996) ACTACRYST. D52, 57-64
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Refinement step | Cycle: LAST / Resolution: 1.4→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.45 Å /
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Refinement | *PLUS Lowest resolution: 10 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.236 / Rfactor Rwork: 0.209 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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