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- PDB-4bnc: Crystal structure of the DNA-binding domain of human ETV1 complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4bnc | |||||||||
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Title | Crystal structure of the DNA-binding domain of human ETV1 complexed with DNA | |||||||||
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![]() | DNA BINDING PROTEIN / DNA-BINDING PROTEIN | |||||||||
Function / homology | ![]() peripheral nervous system neuron development / mechanosensory behavior / muscle organ development / axon guidance / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity ...peripheral nervous system neuron development / mechanosensory behavior / muscle organ development / axon guidance / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription by RNA polymerase II / 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 / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Allerston, C.K. / Cooper, C.D.O. / Krojer, T. / Chaikuad, A. / Vollmar, M. / Froese, D.S. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / von Delft, F. / 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 | ![]() | 74.8 KB | Display | ![]() |
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PDB format | ![]() | 54.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.3 KB | Display | ![]() |
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Full document | ![]() | 434.5 KB | Display | |
Data in XML | ![]() | 6.3 KB | Display | |
Data in CIF | ![]() | 7.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2yprC ![]() 3zp5C ![]() 4avpC ![]() 4co8C ![]() 4unoC ![]() 4uuvC 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: 12437.209 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: DNA chain | Mass: 3094.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: DNA chain | Mass: 2995.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 7.18 Å3/Da / Density % sol: 82.87 % / Description: NONE |
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Crystal grow | Details: SEMET PROTEIN/DNA WAS CRYSTALLISED IN 20%(W/V) PEG 3350 0.2M POTASSIUM CITRATE. NATIVE PROTEIN/DNA WAS CRYSTALLISED IN 28% LMW PEG SMEAR, 100MM TRIS, PH 8.5, 200MM NACL, 5% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 13, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→129.8 Å / Num. obs: 6594 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Biso Wilson estimate: 127.18 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 9.3 % / Rmerge(I) obs: 1.27 / Mean I/σ(I) obs: 1.9 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 2.9→58.02 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.9586 / SU R Cruickshank DPI: 0.442 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.508 / SU Rfree Blow DPI: 0.274 / SU Rfree Cruickshank DPI: 0.266
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Displacement parameters | Biso mean: 123.75 Å2
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Refine analyze | Luzzati coordinate error obs: 0.899 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→58.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.24 Å / Total num. of bins used: 5
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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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