+Open data
-Basic information
Entry | Database: PDB / ID: 1jh5 | ||||||
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Title | Crystal Structure of sTALL-1 of TNF family ligand | ||||||
Components | TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B | ||||||
Keywords | IMMUNE SYSTEM / ANTITUMOR PROTEIN / TALL-1 / BLYS / THANK / BAFF | ||||||
Function / homology | Function and homology information B cell costimulation / positive regulation of germinal center formation / 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 ...B cell costimulation / positive regulation of germinal center formation / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 3 Å | ||||||
Authors | Liu, Y. / Xu, L. / Opalka, N. / Shu, H.-B. / Zhang, G. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2002 Title: Crystal structure of sTALL-1 reveals a virus-like assembly of TNF family ligands. Authors: Liu, Y. / Xu, L. / Opalka, N. / Kappler, J. / Shu, H.B. / Zhang, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jh5.cif.gz | 276.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jh5.ent.gz | 228.2 KB | Display | PDB format |
PDBx/mmJSON format | 1jh5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jh5_validation.pdf.gz | 482.9 KB | Display | wwPDB validaton report |
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Full document | 1jh5_full_validation.pdf.gz | 553.2 KB | Display | |
Data in XML | 1jh5_validation.xml.gz | 56 KB | Display | |
Data in CIF | 1jh5_validation.cif.gz | 73.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jh/1jh5 ftp://data.pdbj.org/pub/pdb/validation_reports/jh/1jh5 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 16244.602 Da / Num. of mol.: 10 / Fragment: sTALL-1, soluble part of TALL-1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y275 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 5.18 Å3/Da / Density % sol: 76.26 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 35% dioxane, pH 9.0, VAPOR DIFFUSION, HANGING DROP at 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. all: 69018 / Num. obs: 66001 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 12 |
Reflection | *PLUS Num. measured all: 334821 |
-Processing
Software |
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Refinement | Resolution: 3→19.99 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 172269.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.285 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 30.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 51752 / % reflection Rfree: 5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 30.6 Å2 | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.344 / % reflection Rfree: 5 % / Rfactor Rwork: 0.331 |