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- PDB-2ypr: Crystal structure of the DNA binding ETS domain of human protein FEV -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ypr | ||||||
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Title | Crystal structure of the DNA binding ETS domain of human protein FEV | ||||||
![]() | PROTEIN FEV | ||||||
![]() | TRANSCRIPTION | ||||||
Function / homology | ![]() neuron fate specification / maternal behavior / neuron maturation / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of gene expression / chromatin ...neuron fate specification / maternal behavior / neuron maturation / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Allerston, C.K. / Cooper, C. / Vollmar, M. / Krojer, T. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Gileadi, O. | ||||||
![]() | ![]() Title: Structures of the Ets Domains of Transcription Factors Etv1, Etv4, Etv5 and Fev: Determinants of DNA Binding and Redox Regulation by Disulfide Bond Formation. Authors: Cooper, C.D.O. / Newman, J.A. / Aitkenhead, H. / Allerston, C.K. / Gileadi, O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89 KB | Display | ![]() |
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PDB format | ![]() | 68.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.2 KB | Display | ![]() |
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Full document | ![]() | 437.8 KB | Display | |
Data in XML | ![]() | 8.6 KB | Display | |
Data in CIF | ![]() | 10.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3zp5C ![]() 4avpC ![]() 4bncC ![]() 4co8C ![]() 4unoC ![]() 4uuvC ![]() 1fliS 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: Protein | Mass: 11813.431 Da / Num. of mol.: 2 / Fragment: ETS DOMAIN, RESIDUES 42-141 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.96 Å3/Da / Density % sol: 68.95 % / Description: NONE |
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Crystal grow | Details: 14% PEG3350, 5% GLYCEROL, 100 MM CITRATE PH 5.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 26, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→75.5 Å / Num. obs: 11808 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 15.9 % / Biso Wilson estimate: 102.82 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 2.64→2.77 Å / Redundancy: 16.8 % / Mean I/σ(I) obs: 2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1FLI Resolution: 2.64→75.5 Å / Cor.coef. Fo:Fc: 0.9357 / Cor.coef. Fo:Fc free: 0.9495 / SU R Cruickshank DPI: 0.289 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.296 / SU Rfree Blow DPI: 0.214 / SU Rfree Cruickshank DPI: 0.213
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Displacement parameters | Biso mean: 87.06 Å2
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Refine analyze | Luzzati coordinate error obs: 0.449 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.64→75.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.64→2.89 Å / Total num. of bins used: 6
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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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