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Yorodumi- PDB-178d: CRYSTAL STRUCTURE OF A DNA DUPLEX CONTAINING 8-HYDROXYDEOXYGUANIN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 178d | ||||||||||||||||||
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Title | CRYSTAL STRUCTURE OF A DNA DUPLEX CONTAINING 8-HYDROXYDEOXYGUANINE.ADENINE BASE-PAIRS | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX / MODIFIED / MISMATCHED | Function / homology | DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | Authors | McAuley-Hecht, K.E. / Leonard, G.A. / Gibson, N.J. / Thomson, J.B. / Watson, W.P. / Hunter, W.N. / Brown, T. | Citation | Journal: Biochemistry / Year: 1994 | Title: Crystal structure of a DNA duplex containing 8-hydroxydeoxyguanine-adenine base pairs. Authors: McAuley-Hecht, K.E. / Leonard, G.A. / Gibson, N.J. / Thomson, J.B. / Watson, W.P. / Hunter, W.N. / Brown, T. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 178d.cif.gz | 24.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb178d.ent.gz | 15.5 KB | Display | PDB format |
PDBx/mmJSON format | 178d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 178d_validation.pdf.gz | 375.9 KB | Display | wwPDB validaton report |
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Full document | 178d_full_validation.pdf.gz | 382.2 KB | Display | |
Data in XML | 178d_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | 178d_validation.cif.gz | 6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/78/178d ftp://data.pdbj.org/pub/pdb/validation_reports/78/178d | HTTPS FTP |
-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: 3703.417 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.99 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 K / pH: 6.5 | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 |
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Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2.5 Å / Num. all: 9923 / Num. obs: 1965 / Observed criterion σ(I): 1 |
Reflection | *PLUS Highest resolution: 2.5 Å / Num. all: 5480 / % possible obs: 81 % / Redundancy: 2.8 % / Num. measured all: 9923 / Rmerge(I) obs: 0.068 |
-Processing
Software | Name: NUCLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.5→10 Å / σ(F): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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Software | *PLUS Name: NUCLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.168 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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