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Open data
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Basic information
Entry | Database: PDB / ID: 3mi8 | ||||||
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Title | The structure of TL1A-DCR3 COMPLEX | ||||||
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Function / homology | ![]() TNFs bind their physiological receptors / activation of NF-kappaB-inducing kinase activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhan, C. / Patskovsky, Y. / Yan, Q. / Li, Z. / Ramagopal, U.A. / Nathenson, S.G. / Almo, S.C. | ||||||
![]() | ![]() Title: Decoy Strategies: The Structure of TL1A:DcR3 Complex. Authors: Zhan, C. / Patskovsky, Y. / Yan, Q. / Li, Z. / Ramagopal, U. / Cheng, H. / Brenowitz, M. / Hui, X. / Nathenson, S.G. / Almo, S.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65.2 KB | Display | ![]() |
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PDB format | ![]() | 46.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3k51SC ![]() 3mhdC 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 20893.684 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 72-251 / Mutation: C135S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 19288.488 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 30-195 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.33 Å3/Da / Density % sol: 71.62 % |
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Crystal grow![]() | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.4M K/Na tartrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 290.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.95→50 Å / Num. all: 15595 / Num. obs: 15595 / Redundancy: 20.9 % / Biso Wilson estimate: 91.4 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 36.6 |
Reflection shell | Resolution: 2.95→3 Å / Redundancy: 21.2 % / Rmerge(I) obs: 0.898 / Mean I/σ(I) obs: 3.9 / Num. unique all: 767 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: pdb entry 3K51 Resolution: 2.951→25.16 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.921 / SU B: 10.413 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.377 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 84.694 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.951→25.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.951→3.027 Å / Total num. of bins used: 20
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