+Open data
-Basic information
Entry | Database: PDB / ID: 231d | ||||||||||||||||||
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Title | STRUCTURE OF A DNA-PORPHYRIN COMPLEX | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / RIGHT HANDED DNA / DOUBLE HELIX / FLIPPED-OUT BASES / COMPLEXED WITH DRUG | Function / homology | CU(II)MESO(4-N-TETRAMETHYLPYRIDYL)PORPHYRIN / DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.4 Å | Authors | Lipscomb, L.A. / Zhou, F.X. / Presnell, S.R. / Woo, R.J. / Peek, M.E. / Plaskon, R.R. / Williams, L.D. | Citation | Journal: Biochemistry / Year: 1996 | Title: Structure of DNA-porphyrin complex. Authors: Lipscomb, L.A. / Zhou, F.X. / Presnell, S.R. / Woo, R.J. / Peek, M.E. / Plaskon, R.R. / Williams, L.D. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 231d.cif.gz | 14.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb231d.ent.gz | 8.7 KB | Display | PDB format |
PDBx/mmJSON format | 231d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/31/231d ftp://data.pdbj.org/pub/pdb/validation_reports/31/231d | 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 on special symmetry positions |
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-Components
#1: DNA chain | Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Chemical | ChemComp-PCU / |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 64.79 % | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 6.5 / Details: pH 6.50, VAPOR DIFFUSION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 6.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 296 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 |
Detector | Type: SDMS / Detector: AREA DETECTOR |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2.3 Å / Num. all: 49552 / Num. obs: 1334 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.4→8 Å / σ(F): 1.5
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Refinement step | Cycle: LAST / Resolution: 2.4→8 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 8 Å / σ(F): 1.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 2.51 Å / Total num. of bins used: 8 / Num. reflection obs: 87 / Rfactor obs: 0.255 |