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Open data
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Basic information
Entry | Database: PDB / ID: 4co8 | ||||||
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Title | Structure of the DNA binding ETS domain of human ETV4 | ||||||
![]() | ETS TRANSLOCATION VARIANT 4 | ||||||
![]() | TRANSCRIPTION | ||||||
Function / homology | ![]() positive regulation of keratinocyte differentiation / MAPK6/MAPK4 signaling / sequence-specific double-stranded DNA binding / chromosome / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / nucleolus ...positive regulation of keratinocyte differentiation / MAPK6/MAPK4 signaling / sequence-specific double-stranded DNA binding / chromosome / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Newman, J.A. / Cooper, C.D.O. / Shrestha, L. / Burgess-Brown, N. / Kopec, J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / 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 | ![]() | 63.5 KB | Display | ![]() |
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PDB format | ![]() | 46 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.2 KB | Display | ![]() |
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Full document | ![]() | 435.8 KB | Display | |
Data in XML | ![]() | 7.7 KB | Display | |
Data in CIF | ![]() | 10.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2yprC ![]() 3zp5C ![]() 4avpC ![]() 4bncSC ![]() 4unoC ![]() 4uuvC 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 15660.855 Da / Num. of mol.: 1 / Fragment: ETS DOMAIN, RESIDUES 338-470 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | FIRST TWO RESIDUES ARE REMAINING FROM CLEAVAGE OF N- TERMINAL HIS TAG | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.61 Å3/Da / Density % sol: 23.57 % / Description: NONE |
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Crystal grow | Details: 0.8 M SODIUM CITRATE TRIBASIC, 0.1 M CACODYLATE PH 6.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→26.8 Å / Num. obs: 46056 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 8.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 1.05→1.07 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.1 / % possible all: 67.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4BNC Resolution: 1.05→43.99 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.547 / SU ML: 0.012 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.022 / 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 mean: 15.559 Å2
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Refinement step | Cycle: LAST / Resolution: 1.05→43.99 Å
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Refine LS restraints |
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