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- PDB-7jsl: 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: 7jsl | |||||||||
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Title | Crystal structure of the DNA binding domain of human transcription factor ERF in the oxidized 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 | ![]() | 130.2 KB | Display | ![]() |
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PDB format | ![]() | 96.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 482.5 KB | Display | ![]() |
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Full document | ![]() | 486.6 KB | Display | |
Data in XML | ![]() | 15.4 KB | Display | |
Data in CIF | ![]() | 21.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7jsaSC 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 3094.042 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthetic DNA / Source: (synth.) synthetic construct (others) #2: DNA chain | Mass: 2995.967 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthetic DNA / Source: (synth.) synthetic construct (others) #3: Protein | Mass: 14222.460 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: The N-terminal region GPHM is a leftover after affinity tag cleavage. The C-terminal region KLVL...SGSS is disordered. Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.41 Å3/Da / Density % sol: 72.1 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 10% PEG 4000, 0.1M Hepes pH 7.5 |
-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: Oct 8, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 4.5→50 Å / Num. obs: 8678 / % possible obs: 99.5 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 4.5→4.58 Å / Num. unique obs: 418 / CC1/2: 0.73 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7JSA Resolution: 4.51→36.85 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.946 / SU B: 71.617 / SU ML: 0.784 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.899 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 347.29 Å2 / Biso mean: 212.875 Å2 / Biso min: 138.21 Å2
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Refinement step | Cycle: final / Resolution: 4.51→36.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.512→4.628 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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