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- PDB-1kxg: The 2.0 Ang Resolution Structure of BLyS, B Lymphocyte Stimulator. -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kxg | ||||||
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Title | The 2.0 Ang Resolution Structure of BLyS, B Lymphocyte Stimulator. | ||||||
![]() | B lymphocyte stimulator | ||||||
![]() | CYTOKINE / BAFF / TALL-1 / THANK / zTNF4 / TNF superfamily / jellyroll / beta-sandwich | ||||||
Function / homology | ![]() positive regulation of germinal center formation / B cell costimulation / TNFs bind their physiological receptors / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / transitional one stage B cell differentiation / germinal center formation / tumor necrosis factor receptor binding / skin development / B cell proliferation / B cell homeostasis ...positive regulation of germinal center formation / B cell costimulation / TNFs bind their physiological receptors / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / transitional one stage B cell differentiation / germinal center formation / tumor necrosis factor receptor binding / skin development / B cell proliferation / B cell homeostasis / T cell proliferation / positive regulation of T cell proliferation / positive regulation of B cell proliferation / tumor necrosis factor-mediated signaling pathway / T cell costimulation / cytokine activity / TNFR2 non-canonical NF-kB pathway / receptor ligand activity / intracellular membrane-bounded organelle / focal adhesion / signaling receptor binding / perinuclear region of cytoplasm / signal transduction / extracellular space / extracellular region / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Oren, D.A. / Li, Y. / Volovik, Y. / Morris, T.S. / Dharia, C. / Das, K. / Galperina, O. / Gentz, R. / Arnold, E. | ||||||
![]() | ![]() Title: Structural basis of BLyS receptor recognition. Authors: Oren, D.A. / Li, Y. / Volovik, Y. / Morris, T.S. / Dharia, C. / Das, K. / Galperina, O. / Gentz, R. / Arnold, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 197.9 KB | Display | ![]() |
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PDB format | ![]() | 156.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 514.9 KB | Display | ![]() |
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Full document | ![]() | 534.9 KB | Display | |
Data in XML | ![]() | 40.4 KB | Display | |
Data in CIF | ![]() | 55.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1d0gS S: Starting model for refinement |
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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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2 | ![]()
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Unit cell |
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Details | The biologically active form is a trimer and two complete trimers are found in the asymmetric unit. |
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Components
#1: Protein | Mass: 17056.443 Da / Num. of mol.: 6 / Fragment: soluble portion (residues 134-285) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | ChemComp-DIO / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 66 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 25% dioxane, 25 mM MgCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 279.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 108 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 13, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.942 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 93234 / % possible obs: 99.3 % / Observed criterion σ(I): -1 / Redundancy: 20.8 % / Rsym value: 0.083 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 2→2.08 Å / Mean I/σ(I) obs: 3.8 / Rsym value: 0.384 / % possible all: 93.8 |
Reflection | *PLUS Highest resolution: 2 Å / Num. measured all: 1940104 / Rmerge(I) obs: 0.083 |
Reflection shell | *PLUS Highest resolution: 2 Å / % possible obs: 93.8 % / Num. unique obs: 9746 / Rmerge(I) obs: 0.384 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1D0G Resolution: 2→24.64 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3298001.29 / Data cutoff high rms absF: 3298001.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: Residues 204-206 in all six chains have very poor electron density.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.31 Å2 / ksol: 0.352931 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Baniso 13: 0 Å2 / Baniso 23: 0 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→24.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 25 Å / Rfactor obs: 0.189 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.223 |