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Yorodumi- PDB-131d: THE LOW-TEMPERATURE CRYSTAL STRUCTURE OF THE PURE-SPERMINE FORM O... -
+Open data
-Basic information
Entry | Database: PDB / ID: 131d | ||||||||||||||||||
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Title | THE LOW-TEMPERATURE CRYSTAL STRUCTURE OF THE PURE-SPERMINE FORM OF Z-DNA REVEALS BINDING OF A SPERMINE MOLECULE IN THE MINOR GROOVE | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / Z-DNA / DOUBLE HELIX | Function / homology | SPERMINE / DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 1 Å | Authors | Bancroft, D. / Williams, L.D. / Rich, A. / Egli, M. | Citation | Journal: Biochemistry / Year: 1994 Title: The low-temperature crystal structure of the pure-spermine form of Z-DNA reveals binding of a spermine molecule in the minor groove. Authors: Bancroft, D. / Williams, L.D. / Rich, A. / Egli, M. #1: Journal: Biochemistry / Year: 1991 Title: Structure of the Pure-Spermine Form of Z-DNA (Magnesium Free) at 1 Angstrom Resolution Authors: Egli, M. / Williams, L.D. / Gao, Q. / Rich, A. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 131d.cif.gz | 19.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb131d.ent.gz | 12 KB | Display | PDB format |
PDBx/mmJSON format | 131d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 131d_validation.pdf.gz | 338.9 KB | Display | wwPDB validaton report |
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Full document | 131d_full_validation.pdf.gz | 352 KB | Display | |
Data in XML | 131d_validation.xml.gz | 3.8 KB | Display | |
Data in CIF | 131d_validation.cif.gz | 4.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/31/131d ftp://data.pdbj.org/pub/pdb/validation_reports/31/131d | 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: 1810.205 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | #3: Chemical | #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: 25.16 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, SITTING DROP / Temp details: ROOM TEMPERATURE | ||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 7 / Details: Egli, M., (1991) Biochemistry, 30, 11388. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 163 K |
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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: 1 Å / Num. all: 14081 / Num. obs: 9691 / Observed criterion σ(F): 2 |
-Processing
Software |
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Refinement | Resolution: 1→5 Å / σ(F): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 1→5 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1 Å / Lowest resolution: 5 Å / Num. reflection obs: 9575 / σ(F): 2 / Rfactor obs: 0.18 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |