+Open data
-Basic information
Entry | Database: PDB / ID: 1k7a | ||||||
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Title | Ets-1(331-440)+GGAG duplex | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / ETS domain / transcription factor / TRANSCRIPTION-DNA COMPLEX | ||||||
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 / cell differentiation / 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) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Garvie, C.W. / Hagman, J. / Wolberger, C. | ||||||
Citation | Journal: Mol.Cell / Year: 2001 Title: Structural studies of Ets-1/Pax5 complex formation on DNA. Authors: Garvie, C.W. / Hagman, J. / Wolberger, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k7a.cif.gz | 80 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k7a.ent.gz | 58.3 KB | Display | PDB format |
PDBx/mmJSON format | 1k7a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k7a_validation.pdf.gz | 457.6 KB | Display | wwPDB validaton report |
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Full document | 1k7a_full_validation.pdf.gz | 465 KB | Display | |
Data in XML | 1k7a_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 1k7a_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k7/1k7a ftp://data.pdbj.org/pub/pdb/validation_reports/k7/1k7a | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 4665.032 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: DNA chain | Mass: 4489.925 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Protein | Mass: 12985.833 Da / Num. of mol.: 2 / Fragment: ETS domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ets-1 / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P27577 |
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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: 2.75 Å3/Da / Density % sol: 55.26 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.4M-1.6M Sodium Citrate, 100mM Hepes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 4.6 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 16, 2001 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→17.04 Å / Num. all: 11730 / Num. obs: 11730 / % possible obs: 0.969 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 76.7 Å2 / Rmerge(I) obs: 0.066 |
Reflection shell | Resolution: 2.8→2.93 Å / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 3.8 / % possible all: 0.989 |
Reflection | *PLUS % possible obs: 96.9 % |
Reflection shell | *PLUS % possible obs: 98.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→17.04 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 785098.7 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 30.2093 Å2 / ksol: 0.363148 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→17.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 17.7 Å / σ(F): 0 / % reflection Rfree: 10.2 % / Rfactor obs: 0.23 / Rfactor Rfree: 0.274 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 52.4 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.396 / Rfactor Rwork: 0.355 |