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- PDB-1ish: Crystal Structure Analysis of BST-1/CD157 complexed with ethenoNADP -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ish | |||||||||
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Title | Crystal Structure Analysis of BST-1/CD157 complexed with ethenoNADP | |||||||||
![]() | bone marrow stromal cell antigen 1 | |||||||||
![]() | HYDROLASE / ADP ribosyl cyclase / NAD glycohydrolase / cns / ethenoNADP | |||||||||
Function / homology | ![]() regulation of cellular extravasation / regulation of superoxide metabolic process / regulation of neutrophil chemotaxis / regulation of integrin-mediated signaling pathway / phosphorus-oxygen lyase activity / Post-translational modification: synthesis of GPI-anchored proteins / uropod / Nicotinate metabolism / regulation of cell-matrix adhesion / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase ...regulation of cellular extravasation / regulation of superoxide metabolic process / regulation of neutrophil chemotaxis / regulation of integrin-mediated signaling pathway / phosphorus-oxygen lyase activity / Post-translational modification: synthesis of GPI-anchored proteins / uropod / Nicotinate metabolism / regulation of cell-matrix adhesion / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD+ nucleotidase, cyclic ADP-ribose generating / humoral immune response / side of membrane / specific granule membrane / regulation of peptidyl-tyrosine phosphorylation / positive regulation of B cell proliferation / regulation of calcium-mediated signaling / regulation of actin cytoskeleton organization / transferase activity / regulation of inflammatory response / positive regulation of cell population proliferation / Neutrophil degranulation / signal transduction / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Yamamoto-Katayama, S. / Ariyoshi, M. / Ishihara, K. / Hirano, T. / Jingami, H. / Morikawa, K. | |||||||||
![]() | ![]() Title: Crystallographic studies on human BST-1/CD157 with ADP-ribosyl cyclase and NAD glycohydrolase activities. Authors: Yamamoto-Katayama, S. / Ariyoshi, M. / Ishihara, K. / Hirano, T. / Jingami, H. / Morikawa, K. #1: ![]() Title: Site-directed removal of N-glycosylation sites in BST-1/CD157: effects on molecular and functional heterogeneity. Authors: Yamamoto-Katayama, S. / Sato, A. / Ariyoshi, M. / Suyama, M. / Ishihara, K. / Hirano, T. / Nakamura, H. / Morikawa, K. / Jingami, H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.2 KB | Display | ![]() |
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PDB format | ![]() | 93.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 24.6 KB | Display | |
Data in CIF | ![]() | 33.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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: 30172.182 Da / Num. of mol.: 2 / Fragment: Extracellular region / Mutation: N34D, N63T, N116A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.62 Å3/Da / Density % sol: 66 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: ammonium sulfate, citrate, ethenoNADP, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: unknown | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 16, 2000 |
Radiation | Monochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.836 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. all: 33495 / Num. obs: 33495 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 30.36 % / Biso Wilson estimate: 44.8 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 3.83 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 17.54 / Num. unique all: 3120 / % possible all: 91.3 |
Reflection | *PLUS Lowest resolution: 20 Å / Rmerge(I) obs: 0.04 |
Reflection shell | *PLUS % possible obs: 91.3 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.6405 Å2 / ksol: 0.38647 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→19.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 7.5 % / Rfactor obs: 0.21 / Rfactor Rwork: 0.21 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 39.5 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.305 / % reflection Rfree: 7.6 % / Rfactor Rwork: 0.26 |