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Yorodumi- PDB-4ix7: Crystal Structure of the insv-BEN domain complexed to its DNA tar... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ix7 | ||||||
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Title | Crystal Structure of the insv-BEN domain complexed to its DNA target site | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / BEN domain / transcriptional repressor / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information chromatin insulator sequence binding / negative regulation of Notch signaling pathway / transcription corepressor activity / sequence-specific DNA binding / negative regulation of DNA-templated transcription / nucleus Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.581 Å | ||||||
Authors | Ren, A. / Serganov, A. / Patel, D.J. | ||||||
Citation | Journal: Genes Dev. / Year: 2013 Title: The BEN domain is a novel sequence-specific DNA-binding domain conserved in neural transcriptional repressors. Authors: Dai, Q. / Ren, A. / Westholm, J.O. / Serganov, A.A. / Patel, D.J. / Lai, E.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ix7.cif.gz | 73.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ix7.ent.gz | 58.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ix7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/4ix7 ftp://data.pdbj.org/pub/pdb/validation_reports/ix/4ix7 | HTTPS FTP |
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-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: 3990.622 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Protein | Mass: 13054.505 Da / Num. of mol.: 2 / Fragment: Insv-BEN domain (UNP residues 251-365) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG3227, insensitive, insv / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8SYK5 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M MES, pH 6.5, 26% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9789 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2011 |
Radiation | Monochromator: Rosenbaum-Rock double crystal sagittal focusing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→50 Å / Num. all: 41090 / Num. obs: 41021 / % possible obs: 99.8 % / Redundancy: 14.4 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 59.6 |
Reflection shell | Resolution: 1.58→1.61 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.712 / Mean I/σ(I) obs: 4 / Rsym value: 0.712 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.581→39.063 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 20.68 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.434 Å2 / ksol: 0.374 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.581→39.063 Å
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Refine LS restraints |
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LS refinement shell |
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