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Yorodumi- PDB-5e8i: Crystal structure of the DNA binding domain of human transcriptio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5e8i | ||||||
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Title | Crystal structure of the DNA binding domain of human transcription factor FLI1 in complex with a 10-mer DNA ACCGGAAGTG | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / Transcription / DNA binding / Ewing sarcoma / Winged helix / ETS family / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information hemostasis / blood circulation / megakaryocyte development / animal organ morphogenesis / Transcriptional regulation of granulopoiesis / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear body / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific ...hemostasis / blood circulation / megakaryocyte development / animal organ morphogenesis / Transcriptional regulation of granulopoiesis / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear body / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Endothia gyrosa (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å | ||||||
Authors | Hou, C. / Tsodikov, O.V. | ||||||
Citation | Journal: Biochemistry / Year: 2015 Title: Structural Basis for Dimerization and DNA Binding of Transcription Factor FLI1. Authors: Hou, C. / Tsodikov, O.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e8i.cif.gz | 136.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e8i.ent.gz | 100.2 KB | Display | PDB format |
PDBx/mmJSON format | 5e8i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/5e8i ftp://data.pdbj.org/pub/pdb/validation_reports/e8/5e8i | HTTPS FTP |
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-Related structure data
Related structure data | 5e8gC 4iriS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 14946.829 Da / Num. of mol.: 4 / Fragment: UNP residues 276-399 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FLI1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q01543 #2: DNA chain | Mass: 3094.042 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Endothia gyrosa (fungus) #3: DNA chain | Mass: 2995.967 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Endothia gyrosa (fungus) #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | |
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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: 2.97 Å3/Da / Density % sol: 58.52 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Na cacodylate pH 6.5, 0.2 M CaCl2, 14% w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HS / Detector: CCD / Date: Aug 5, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.45→50 Å / Num. obs: 13800 / % possible obs: 99.9 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 19 |
Reflection shell | Resolution: 3.45→3.51 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.9 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IRI Resolution: 3.45→35 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU B: 37.095 / SU ML: 0.517 / Cross valid method: THROUGHOUT / ESU R Free: 0.577 / 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: 133.671 Å2
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Refinement step | Cycle: 1 / Resolution: 3.45→35 Å
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Refine LS restraints |
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