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Open data
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Basic information
Entry | Database: PDB / ID: 6mng | ||||||
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Title | 4738 TCR bound to IAb Padi4 | ||||||
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Function / homology | ![]() positive regulation of antigen processing and presentation / positive regulation of alpha-beta T cell activation / Chromatin modifying enzymes / histone H3R2 arginine deiminase activity / histone H3R8 arginine deiminase activity / histone H3R17 arginine deiminase activity / histone arginine deiminase activity / histone H3R26 arginine deiminase activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Blevins, S.J. / Stadinski, B.D. / Huseby, E.S. | ||||||
![]() | ![]() Title: A temporal thymic selection switch and ligand binding kinetics constrain neonatal Foxp3+Tregcell development. Authors: Stadinski, B.D. / Blevins, S.J. / Spidale, N.A. / Duke, B.R. / Huseby, P.G. / Stern, L.J. / Huseby, E.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 | ![]() | 170.7 KB | Display | ![]() |
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PDB format | ![]() | 128.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6mkdC ![]() 6mkrC ![]() 6mnmC ![]() 6mnnC ![]() 6mnoC ![]() 4p23S 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 | Mass: 20242.615 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 25027.908 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: Q9Z183, UniProt: P14483, ![]() |
#3: Protein | Mass: 23208.652 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
#4: Protein | Mass: 26756.602 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
#5: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.6 % / Mosaicity: 0.1 ° |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: 12% PEG 4000, 100mM NaCacodylate, 100 mM NaCitrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.66→29.66 Å / Num. obs: 31505 / % possible obs: 99.1 % / Redundancy: 6.9 % / Biso Wilson estimate: 56.95 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.044 / Rrim(I) all: 0.118 / Net I/σ(I): 11.6 / Num. measured all: 218095 |
Reflection shell | Resolution: 2.66→2.73 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.761 / Num. unique obs: 2074 / CC1/2: 0.878 / Rpim(I) all: 0.306 / Rrim(I) all: 0.821 / % possible all: 90.7 |
-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4P23 Resolution: 2.662→29.66 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.67
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 118.6 Å2 / Biso mean: 50.2462 Å2 / Biso min: 20 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.662→29.66 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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