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- PDB-6xnf: GCN4-p1 Peptide Trimer with Tetrafluoroiodophenylalanine residue ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6xnf | |||||||||
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Title | GCN4-p1 Peptide Trimer with Tetrafluoroiodophenylalanine residue at position 16 (TFI-F16) | |||||||||
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![]() | TRANSCRIPTION / Coil-coil / tetrafluoroiodo-modified phenylalanine | |||||||||
Function / homology | ![]() protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding ...protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / amino acid biosynthetic process / cellular response to amino acid starvation / RNA polymerase II transcription regulator complex / : / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Rowe Hartje, R.K. / Czarny, R.S. / Ho, A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Engineering Specific Protein-Protein Interactions Through Halogen and Hydrogen Bonds Authors: Rowe Hartje, R.K. / Ferrero, M. / Cavallo, G. / Metrangolo, P. / Ho, A. / Czarny, R. / Ho, P.S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.6 KB | Display | ![]() |
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PDB format | ![]() | 40.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423.6 KB | Display | ![]() |
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Full document | ![]() | 425.7 KB | Display | |
Data in XML | ![]() | 4.8 KB | Display | |
Data in CIF | ![]() | 6.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6xneC ![]() 6xnlC ![]() 6xnmC ![]() 1swiS 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/peptide | Mass: 3893.234 Da / Num. of mol.: 1 / Mutation: TFI-F16 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() | ||||||
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#2: Protein/peptide | Mass: 3619.280 Da / Num. of mol.: 2 / Mutation: TFI-F16 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #3: Chemical | ChemComp-NA / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.54 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Crystallization drops were prepared by mixing 2 uL of stock peptide solution with 2 uL of mother liquor and allowed to equilibrate at 298 K over a well containing 500 uL of mother liquor. ...Details: Crystallization drops were prepared by mixing 2 uL of stock peptide solution with 2 uL of mother liquor and allowed to equilibrate at 298 K over a well containing 500 uL of mother liquor. The stock peptide solution (total concentration 1.5 mM) was prepared by mixing 2:1 ratios of the A16 peptide with TFI-F16 in 10 mM potassium phosphate, 100 mM potassium chloride pH 7.0. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Aug 8, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→46.21 Å / Num. obs: 43081 / % possible obs: 99.47 % / Redundancy: 6.5 % / Biso Wilson estimate: 28.81 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.09809 / Rpim(I) all: 0.04159 / Rrim(I) all: 0.1068 / Net I/σ(I): 11.38 |
Reflection shell | Resolution: 2→2.072 Å / Redundancy: 6 % / Rmerge(I) obs: 0.7578 / Mean I/σ(I) obs: 2.69 / Num. unique obs: 3998 / CC1/2: 0.766 / CC star: 0.931 / Rpim(I) all: 0.8326 / Rrim(I) all: 0.3375 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1SWI Resolution: 2→46.21 Å / SU ML: 0.2044 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.4397 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: 39.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→46.21 Å
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Refine LS restraints |
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LS refinement shell |
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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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