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Yorodumi- PDB-1d26: EFFECT OF A SINGLE 3'-METHYLENE PHOSPHONATE LINKAGE ON THE CONFOR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d26 | ||||||||||||||||||
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Title | EFFECT OF A SINGLE 3'-METHYLENE PHOSPHONATE LINKAGE ON THE CONFORMATION OF AN A-DNA OCTAMER DOUBLE HELIX | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / A-DNA / DOUBLE HELIX / MODIFIED | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.12 Å | Authors | Heinemann, U. | Citation | Journal: Nucleic Acids Res. / Year: 1991 Title: Effect of a single 3'-methylene phosphonate linkage on the conformation of an A-DNA octamer double helix. Authors: Heinemann, U. / Rudolph, L.N. / Alings, C. / Morr, M. / Heikens, W. / Frank, R. / Blocker, H. #1: Journal: Structure and Methods. DNA and RNA / Year: 1990 Title: Structural Features of G/C-Rich DNA Going A or B Authors: Heinemann, U. / Alings, C. / Lauble, H. #2: Journal: Nucleosides and Nucleotides / Year: 1990 Title: X-Ray Studies of DNA Aiming at Elucidating the Sequence-Structure Code Authors: Heinemann, U. / Alings, C. / Lauble, H. #3: Journal: Nucleosides and Nucleotides / Year: 1988 Title: X-Ray Crystallographic Studies of the A-Form of DNA Authors: Heinemann, U. / Lauble, H. / Frank, R. / Bloecker, H. #4: Journal: Nucleic Acids Res. / Year: 1987 Title: Crystal Structure Analysis of an A-DNA Fragment at 1.8 Angstroms Resolution: d(GCCCGGGC) Authors: Heinemann, U. / Lauble, H. / Frank, R. / Bloecker, H. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d26.cif.gz | 14 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d26.ent.gz | 8.3 KB | Display | PDB format |
PDBx/mmJSON format | 1d26.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/1d26 ftp://data.pdbj.org/pub/pdb/validation_reports/d2/1d26 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 2426.620 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.06 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: microdialysis / pH: 7 / Details: pH 7.00, MICRODIALYSIS, temperature 277.00K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 |
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Detector | Type: ARNDT-WONACOTT / Detector: OSCILLATION CAMERA |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.12→6 Å / Num. obs: 1303 / Observed criterion σ(F): 1 |
-Processing
Software | Name: NUCLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.12→6 Å / σ(F): 3 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 2.12→6 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.12 Å / Lowest resolution: 6 Å / Num. reflection obs: 1197 / σ(I): 3 / Rfactor obs: 0.16 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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