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Yorodumi- PDB-1d40: BASE SPECIFIC BINDING OF COPPER(II) TO Z-DNA: THE 1.3-ANGSTROMS S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d40 | ||||||||||||||||||
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Title | BASE SPECIFIC BINDING OF COPPER(II) TO Z-DNA: THE 1.3-ANGSTROMS SINGLE CRYSTAL STRUCTURE OF D(M5CGUAM5CG) IN THE PRESENCE OF CUCL2 | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / Z-DNA / DOUBLE HELIX / MODIFIED | Function / homology | COPPER (II) ION / COPPER (II) CHLORIDE / DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 1.3 Å | Authors | Geierstanger, B.H. / Kagawa, T.F. / Chen, S.-L. / Quigley, G.J. / Ho, P.S. | Citation | Journal: J.Biol.Chem. / Year: 1991 Title: Base-specific binding of copper(II) to Z-DNA. The 1.3-A single crystal structure of d(m5CGUAm5CG) in the presence of CuCl2. Authors: Geierstanger, B.H. / Kagawa, T.F. / Chen, S.L. / Quigley, G.J. / Ho, P.S. #1: Journal: Biochemistry / Year: 1990 Title: Stabilization of Z-DNA by Demethylation of Thymine Bases: 1.3-Angstroms Single-Crystal Structure of d(m5CGUAm5CG) Authors: Zhou, G. / Ho, P.S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d40.cif.gz | 22.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d40.ent.gz | 13.2 KB | Display | PDB format |
PDBx/mmJSON format | 1d40.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d40_validation.pdf.gz | 373.6 KB | Display | wwPDB validaton report |
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Full document | 1d40_full_validation.pdf.gz | 398 KB | Display | |
Data in XML | 1d40_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | 1d40_validation.cif.gz | 7.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/1d40 ftp://data.pdbj.org/pub/pdb/validation_reports/d4/1d40 | 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: 1823.245 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | #3: Chemical | ChemComp-CUL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.64 Å3/Da / Density % sol: 25.08 % | |||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION / Temp details: ROOM TEMPERATURE | |||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion / Details: took Zhou and Ho, 1990 from original paper | |||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Ambient temp details: ROOM TEMPERATURE |
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Detector | Type: ENRAF-NONIUS / Detector: AREA DETECTOR |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 1.3 Å / Num. obs: 2587 / Observed criterion σ(I): 2 |
Reflection | *PLUS Highest resolution: 1.3 Å / Num. all: 4357 / Observed criterion σ(I): 2 |
-Processing
Software | Name: NUCLSQ / Classification: refinement | ||||||||||||
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Refinement | Starting model: ZDFB24 Highest resolution: 1.3 Å / σ(I): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Highest resolution: 1.3 Å
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Refinement | *PLUS Highest resolution: 1.3 Å / Num. reflection obs: 2587 / σ(F): 2 / Rfactor obs: 0.209 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |