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- PDB-7jsa: Crystal structure of the DNA binding domain of human transcriptio... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7jsa | |||||||||
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Title | Crystal structure of the DNA binding domain of human transcription factor ERF in the reduced form, in complex with double-stranded DNA ACCGGAAGTG | |||||||||
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![]() | DNA BINDING PROTEIN/DNA / Transcription / Tumor suppressor / ETS family / repressor / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | |||||||||
Function / homology | ![]() Oncogene Induced Senescence / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific DNA binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Hou, C. / Tsodikov, O.V. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Insight into the DNA Binding Function of Transcription Factor ERF. Authors: Hou, C. / McCown, C. / Ivanov, D.N. / Tsodikov, O.V. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.6 KB | Display | ![]() |
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PDB format | ![]() | 54.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437 KB | Display | ![]() |
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Full document | ![]() | 437.1 KB | Display | |
Data in XML | ![]() | 6 KB | Display | |
Data in CIF | ![]() | 7.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7jslC ![]() 6jvtS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 3094.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 2995.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA / Source: (synth.) synthetic construct (others) |
#3: Protein | Mass: 14222.460 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The N-terminal region GPHM is an N-terminal tag leftover after cleavage. The C-terminal region starting with KLVL... is disordered. Source: (gene. exp.) ![]() ![]() ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 64.29 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 6% PEG 4000, 0.1M Hepes, 7.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→50 Å / Num. obs: 7139 / % possible obs: 99.9 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 32 |
Reflection shell | Resolution: 2.85→2.9 Å / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.06 / Num. unique obs: 348 / CC1/2: 0.89 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6JVT Resolution: 2.85→37.75 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.882 / SU B: 33.081 / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.54 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 163.88 Å2 / Biso mean: 84.67 Å2 / Biso min: 55.96 Å2
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Refinement step | Cycle: final / Resolution: 2.85→37.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.853→2.926 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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