+Open data
-Basic information
Entry | Database: PDB / ID: 9bdy | ||||||
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Title | AT-centric NF-kappaB RelA binding DNA | ||||||
Components |
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Keywords | DNA / kappaB DNA / Promoter / Transcription / RelA | ||||||
Function / homology | ACETATE ION / DNA / DNA (> 10) Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å | ||||||
Authors | Biswas, T. / Shahabi, S. / Tsodikov, O.V. / Ghosh, G. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2024 Title: Transient interactions modulate the affinity of NF-kappa B transcription factors for DNA. Authors: Li, T. / Shahabi, S. / Biswas, T. / Tsodikov, O.V. / Pan, W. / Huang, D.B. / Wang, V.Y. / Wang, Y. / Ghosh, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9bdy.cif.gz | 167.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9bdy.ent.gz | 125.1 KB | Display | PDB format |
PDBx/mmJSON format | 9bdy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9bdy_validation.pdf.gz | 492.9 KB | Display | wwPDB validaton report |
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Full document | 9bdy_full_validation.pdf.gz | 497.8 KB | Display | |
Data in XML | 9bdy_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 9bdy_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bd/9bdy ftp://data.pdbj.org/pub/pdb/validation_reports/bd/9bdy | HTTPS FTP |
-Related structure data
Related structure data | 9bduC 9bdvC 9bdwC 9bdxC 9bdzC 9be0C 9be1C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
-Components
#1: DNA chain | Mass: 3687.417 Da / Num. of mol.: 12 / Source method: obtained synthetically Details: Each chain is two separate complementary DNA oligomers: CGGGAAATTCCG and CGGAATTTCCCG Source: (synth.) Homo sapiens (human) #2: DNA chain | Mass: 3638.379 Da / Num. of mol.: 12 / Source method: obtained synthetically Details: Each chain is two separate complementary DNA oligomers: CGGGAAATTCCG and CGGAATTTCCCG Source: (synth.) Homo sapiens (human) #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-ACT / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: PEG3350 8%, Sodium Acetate pH 3.5 100 mM, 50 mM Zinc Acetate |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 8, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 13215 / % possible obs: 81.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.09 / Χ2: 0.103 / Net I/σ(I): 13.1 / Num. measured all: 72351 |
Reflection shell | Resolution: 2.8→2.87 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1124 / Χ2: 0.444 / % possible all: 67.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.907 / SU B: 21.45 / SU ML: 0.423 / Cross valid method: THROUGHOUT / ESU R Free: 0.703 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.774 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→30 Å
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