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- PDB-6xnl: GCN4-p1 Peptide Trimer with iodo-phenylalanine residue at positio... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6xnl | |||||||||
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Title | GCN4-p1 Peptide Trimer with iodo-phenylalanine residue at position 16 (IPF-F16) | |||||||||
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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 / ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 60.4 KB | Display | ![]() |
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PDB format | ![]() | 37.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6xneC ![]() 6xnfC ![]() 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 on special symmetry positions |
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Components
#1: Protein/peptide | Mass: 3821.272 Da / Num. of mol.: 1 / Mutation: IPF-F16 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() ![]() | ||||||
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#2: Protein/peptide | Mass: 3619.280 Da / Num. of mol.: 2 / Mutation: N16A / Source method: obtained synthetically / Source: (synth.) ![]() ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.46 % |
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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 IPF-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: RDI CMOS_8M / Detector: CMOS / Date: Jan 9, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.2→19.85 Å / Num. obs: 8716 / % possible obs: 97.92 % / Redundancy: 1.8 % / Biso Wilson estimate: 34.53 Å2 / CC1/2: 0.986 / CC star: 0.997 / Rmerge(I) obs: 0.07098 / Rpim(I) all: 0.07098 / Rrim(I) all: 0.1004 / Net I/σ(I): 14.32 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.4292 / Mean I/σ(I) obs: 2.67 / Num. unique obs: 695 / CC1/2: 0.462 / Rpim(I) all: 0.4292 / Rrim(I) all: 0.607 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1SWI Resolution: 2.2→19.85 Å / SU ML: 0.4276 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.59 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: 45.74 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→19.85 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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