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Open data
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Basic information
Entry | Database: PDB / ID: 5znz | ||||||
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Title | Structure of mDR3 DD with MBP tag mutant-I387V | ||||||
![]() | Maltose-binding periplasmic protein,Tumor necrosis factor receptor superfamily, member 25 | ||||||
![]() | APOPTOSIS / TNFRSF25 / TRADD / NF-kappa B | ||||||
Function / homology | ![]() TNFs bind their physiological receptors / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex ...TNFs bind their physiological receptors / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / apoptotic process / signal transduction / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jin, T. / Yin, X. | ||||||
![]() | ![]() Title: Crystal structure and activation mechanism of DR3 death domain. Authors: Yin, X. / Li, W. / Ma, H. / Zeng, W. / Peng, C. / Li, Y. / Liu, M. / Chen, Q. / Zhou, R. / Jin, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 694.1 KB | Display | ![]() |
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PDB format | ![]() | 580.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5yevC ![]() 5ygpC ![]() 5ygsC ![]() 5znyC ![]() 1ompS 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 | Mass: 51356.250 Da / Num. of mol.: 4 Mutation: D108A,K109A,E198A,N199A,K265A,E385A,K388A,D389A,I387V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() Strain: K12 / Gene: malE, b4034, JW3994, Tnfrsf25, mCG_4090 / Production host: ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.03 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 2.5 M ammonium sulfate, 0.1 M MES 5.5 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 25, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→50 Å / Num. obs: 75446 / % possible obs: 99.5 % / Redundancy: 6.53 % / CC1/2: 0.999 / Net I/σ(I): 17.51 |
Reflection shell | Resolution: 2.55→2.7 Å / CC1/2: 0.806 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1OMP Resolution: 2.55→47.527 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.55→47.527 Å
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LS refinement shell | Resolution: 2.55→2.641 Å | ||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 45.1365 Å / Origin y: -3.772 Å / Origin z: -43.6477 Å
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Refinement TLS group | Selection details: all |