+Open data
-Basic information
Entry | Database: PDB / ID: 1sgs | ||||||
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Title | Crystal structure of a free kB DNA | ||||||
Components | kB DNA | ||||||
Keywords | DNA / free kB DNA / Calcium binding / NF-kB binding | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Huang, D.B. / Phelps, C.B. / Fusco, A.J. / Ghosh, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Crystal structure of a free kappaB DNA: insights into DNA recognition by transcription factor NF-kappaB. Authors: Huang, D.B. / Phelps, C.B. / Fusco, A.J. / Ghosh, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sgs.cif.gz | 24.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sgs.ent.gz | 15 KB | Display | PDB format |
PDBx/mmJSON format | 1sgs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sg/1sgs ftp://data.pdbj.org/pub/pdb/validation_reports/sg/1sgs | HTTPS FTP |
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-Related structure data
Related structure data | 1ramS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Details | The second part of the biological assembly is generated by a two fold axis in R32 space group |
-Components
#1: DNA chain | Mass: 5187.373 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The protein was chemically synthesized. The sequence of the protein naturally occurs in Homo sapiens (human). | ||
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#2: Chemical | ChemComp-CA / #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: 2.23 Å3/Da / Density % sol: 44.9 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 3350, BOG, CaCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Jul 1, 2003 / Details: mirrors |
Radiation | Monochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. all: 6411 / Num. obs: 6341 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 37 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.39 / Net I/σ(I): 29.4 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 12 / % possible all: 91.3 |
Reflection | *PLUS % possible obs: 99 % / Num. measured all: 242967 / Rmerge(I) obs: 0.039 |
Reflection shell | *PLUS % possible obs: 91 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 12 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1RAM Resolution: 1.6→14.37 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1003948.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.4827 Å2 / ksol: 0.380301 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→14.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 30 Å / Num. reflection obs: 6340 / % reflection Rfree: 10 % / Rfactor Rfree: 0.215 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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