+Open data
-Basic information
Entry | Database: PDB / ID: 6da1 | ||||||
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Title | ETS1 in complex with synthetic SRR mimic | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / ETS1 / transcription factor / complex / autoinhibition | ||||||
Function / homology | Function and homology information Oncogene Induced Senescence / regulation of extracellular matrix disassembly / histone acetyltransferase binding / immune system process / regulation of angiogenesis / positive regulation of endothelial cell migration / positive regulation of erythrocyte differentiation / negative regulation of inflammatory response / positive regulation of angiogenesis / sequence-specific double-stranded DNA binding ...Oncogene Induced Senescence / regulation of extracellular matrix disassembly / histone acetyltransferase binding / immune system process / regulation of angiogenesis / positive regulation of endothelial cell migration / positive regulation of erythrocyte differentiation / negative regulation of inflammatory response / positive regulation of angiogenesis / sequence-specific double-stranded DNA binding / DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / nucleic acid binding / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of cell migration / DNA-binding transcription factor activity / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.0001269892 Å | ||||||
Authors | Perez-Borrajero, C. / Okon, M. / Lin, C.S. / Scheu, K. / Murphy, M.E.P. / Graves, B.J. / McIntosh, L.P. | ||||||
Citation | Journal: J. Mol. Biol. / Year: 2019 Title: The Biophysical Basis for Phosphorylation-Enhanced DNA-Binding Autoinhibition of the ETS1 Transcription Factor. Authors: Perez-Borrajero, C. / Lin, C.S. / Okon, M. / Scheu, K. / Graves, B.J. / Murphy, M.E.P. / McIntosh, L.P. #1: Journal: J. Appl. Crystallogr. / Year: 2007 Title: Phaser crystallographic software Authors: McCoy, A.J. / Grosse-Kunstleve, R.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6da1.cif.gz | 230.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6da1.ent.gz | 158.5 KB | Display | PDB format |
PDBx/mmJSON format | 6da1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6da1_validation.pdf.gz | 449.4 KB | Display | wwPDB validaton report |
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Full document | 6da1_full_validation.pdf.gz | 449.4 KB | Display | |
Data in XML | 6da1_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 6da1_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/6da1 ftp://data.pdbj.org/pub/pdb/validation_reports/da/6da1 | HTTPS FTP |
-Related structure data
Related structure data | 6datC 1md0S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16268.591 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ets1, Ets-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P27577 #2: Protein/peptide | | Mass: 2408.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.42 % / Description: cubic |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: PEG 3350, lithium sulfate, ethylene glycol, MES / PH range: 7.0-8.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97952 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97952 Å / Relative weight: 1 |
Reflection | Resolution: 2→65.24 Å / Num. obs: 26181 / % possible obs: 100 % / Redundancy: 11.1 % / Biso Wilson estimate: 41.0002441188 Å2 / CC1/2: 0.999 / R split: 0.04 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.038 / Rrim(I) all: 0.094 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2→2.05 Å / Rmerge(I) obs: 1.898 / CC1/2: 0.938 / Rpim(I) all: 0.55 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MD0 Resolution: 2.0001269892→56.7828354451 Å / SU ML: 0.235777847374 / Cross valid method: FREE R-VALUE / σ(F): 1.33645593417 / Phase error: 27.1600854185 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.1587261361 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.0001269892→56.7828354451 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 35.9793539016 Å / Origin y: 38.0181356515 Å / Origin z: 28.9284815153 Å
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Refinement TLS group | Selection details: all |