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Yorodumi- PDB-128d: MOLECULAR STRUCTURE OF D(CGC[E6G]AATTCGCG) COMPLEXED WITH HOECHST... -
+Open data
-Basic information
Entry | Database: PDB / ID: 128d | ||||||||||||||||||
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Title | MOLECULAR STRUCTURE OF D(CGC[E6G]AATTCGCG) COMPLEXED WITH HOECHST 33258 | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG / MODIFIED | Function / homology | Chem-HT / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | Authors | Sriram, M. / Van Der Marel, G.A. / Roelen, H.L.P.F. / Van Boom, J.H. / Wang, A.H.-J. | Citation | Journal: EMBO J. / Year: 1992 | Title: Conformation of B-DNA containing O6-ethyl-G-C base pairs stabilized by minor groove binding drugs: molecular structure of d(CGC[e6G]AATTCGCG complexed with Hoechst 33258 or Hoechst 33342. Authors: Sriram, M. / van der Marel, G.A. / Roelen, H.L. / van Boom, J.H. / Wang, A.H. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 128d.cif.gz | 26.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb128d.ent.gz | 16.4 KB | Display | PDB format |
PDBx/mmJSON format | 128d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 128d_validation.pdf.gz | 401 KB | Display | wwPDB validaton report |
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Full document | 128d_full_validation.pdf.gz | 426 KB | Display | |
Data in XML | 128d_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | 128d_validation.cif.gz | 8.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/28/128d ftp://data.pdbj.org/pub/pdb/validation_reports/28/128d | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3691.445 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-HT / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.81 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION / Temp details: ROOM TEMPERATURE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Ambient temp details: ROOM TEMPERATURE |
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Diffraction source | Source: ROTATING ANODE |
Detector | Type: RIGAKU AFC-5R / Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2.5 Å / Num. obs: 1225 / Observed criterion σ(F): 2 |
-Processing
Software | Name: NUCLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Highest resolution: 2.5 Å / σ(F): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Highest resolution: 2.5 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.5 Å / Num. reflection obs: 1225 / σ(F): 3 / Rfactor obs: 0.145 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: n_bond_d / Dev ideal: 0.02 |