+Open data
-Basic information
Entry | Database: PDB / ID: 9bdz | ||||||
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Title | TA-centric NF-kappaB RelA binding DNA | ||||||
Components | (double-stranded DNA) x 2 | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Biswas, T. / Shahabi, S. / Tsodikov, O.V. / Wang, 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 | 9bdz.cif.gz | 174.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9bdz.ent.gz | 130 KB | Display | PDB format |
PDBx/mmJSON format | 9bdz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9bdz_validation.pdf.gz | 475.9 KB | Display | wwPDB validaton report |
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Full document | 9bdz_full_validation.pdf.gz | 481.5 KB | Display | |
Data in XML | 9bdz_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 9bdz_validation.cif.gz | 28.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bd/9bdz ftp://data.pdbj.org/pub/pdb/validation_reports/bd/9bdz | HTTPS FTP |
-Related structure data
Related structure data | 9bduC 9bdvC 9bdwC 9bdxC 9bdyC 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: 3678.403 Da / Num. of mol.: 12 / Source method: obtained synthetically Details: Each chain is two separate complementary DNA oligomers: CGGGAATTTCCG and CGGAAATTCCCG Source: (synth.) Homo sapiens (human) #2: DNA chain | Mass: 3647.393 Da / Num. of mol.: 12 / Source method: obtained synthetically Details: Each chain is two separate complementary DNA oligomers: CGGGAATTTCCG and CGGAAATTCCCG 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: 2.06 Å3/Da / Density % sol: 40.28 % |
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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: 3→50 Å / Num. obs: 12092 / % possible obs: 88.9 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.625 / Num. unique obs: 1100 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.894 / SU B: 24.401 / SU ML: 0.452 / Cross valid method: THROUGHOUT / ESU R Free: 0.759 / 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: 44.472 Å2
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Refinement step | Cycle: 1 / Resolution: 3→30 Å
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