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Open data
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Basic information
Entry | Database: PDB / ID: 7kp7 | ||||||
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Title | asymmetric mTNF-alpha hTNFR1 complex | ||||||
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Function / homology | ![]() TNF signaling / negative regulation of alkaline phosphatase activity / TNFR1-mediated ceramide production / TNFR1-induced proapoptotic signaling / positive regulation of amide metabolic process / cellular extravasation / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Arakaki, T.L. / Fox III, D. / Edwards, T.E. / Foley, A. / Ceska, T. | ||||||
![]() | ![]() Title: Structural insights into the disruption of TNF-TNFR1 signalling by small molecules stabilising a distorted TNF. Authors: McMillan, D. / Martinez-Fleites, C. / Porter, J. / Fox 3rd, D. / Davis, R. / Mori, P. / Ceska, T. / Carrington, B. / Lawson, A. / Bourne, T. / O'Connell, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 185 KB | Display | ![]() |
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PDB format | ![]() | 147 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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: 16411.596 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Protein | ![]() Mass: 16196.158 Da / Num. of mol.: 3 / Mutation: N25D, C153S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-SO4 / ![]() #4: Sugar | ChemComp-NAG / ![]() #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.98 Å3/Da / Density % sol: 69.07 % |
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Crystal grow![]() | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 2.0M Ammonium sulfate, 0.1M BisTris pH5.5, and cryo-protected with paraffin oil; Vapor diffusion, sitting drop, temperature 289K. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 11, 2014 |
Radiation | Monochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.65→50 Å / Num. obs: 43935 / % possible obs: 99.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 49.2 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 19.98 |
Reflection shell | Resolution: 2.65→2.72 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 2.83 / Num. unique obs: 3238 / % possible all: 99.5 |
-Phasing
Phasing![]() | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: unpublished structure Resolution: 2.65→49.07 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.923 / SU B: 9.446 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.366 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.464 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→49.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.719 Å / Total num. of bins used: 20
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