+Open data
-Basic information
Entry | Database: PDB / ID: 1zjf | ||||||
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Title | 12mer-spd-P4N | ||||||
Components |
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Keywords | DNA / flipped-out bases / A-DNA / P4N | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Dohm, J.A. / Hsu, M.H. / Hwu, J.R. / Huang, R.C. / Moudrianakis, E.N. / Lattman, E.E. / Gittis, A.G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Influence of Ions, Hydration, and the Transcriptional Inhibitor P4N on the Conformations of the Sp1 Binding Site. Authors: Dohm, J.A. / Hsu, M.H. / Hwu, J.R. / Huang, R.C. / Moudrianakis, E.N. / Lattman, E.E. / Gittis, A.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zjf.cif.gz | 20.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zjf.ent.gz | 13.9 KB | Display | PDB format |
PDBx/mmJSON format | 1zjf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/1zjf ftp://data.pdbj.org/pub/pdb/validation_reports/zj/1zjf | HTTPS FTP |
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-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: 3784.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ordered from Biosource |
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#2: DNA chain | Mass: 3544.308 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ordered from Biosource |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 64 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: PEG 400, spermidine, bis tris propane, sodium chloride, P4N, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 3873 / Num. obs: 3846 / % possible obs: 99.3 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 |
Reflection shell | Resolution: 2.2→2.28 Å / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→20 Å / σ(F): 0 / Stereochemistry target values: CNS nucleic acid files Details: The crystals were grown in the presence of spermidine and P4N, but these components are not visualized in the maps.
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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