+Open data
-Basic information
Entry | Database: PDB / ID: 1uhx | ||||||||||||||||||
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Title | Crystal structure of d(GCGAGAGC): the base-intercalated duplex | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / base-intercalated duplex / base-intercalated motif / sheared G:A pair / Deoxyribonucleic acid | Function / homology | COBALT HEXAMMINE(III) / DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | Authors | Kondo, J. / Umeda, S.I. / Fujita, K. / Sunami, T. / Takenaka, A. | Citation | Journal: J.Synchrotron Radiat. / Year: 2004 | 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uhx.cif.gz | 16.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uhx.ent.gz | 9.9 KB | Display | PDB format |
PDBx/mmJSON format | 1uhx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uh/1uhx ftp://data.pdbj.org/pub/pdb/validation_reports/uh/1uhx | 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
-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
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å |
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 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 3 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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