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Yorodumi- PDB-4nsb: Crystal structure of the complex of signaling glycoprotein, SPB-4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nsb | ||||||
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Title | Crystal structure of the complex of signaling glycoprotein, SPB-40 and N-acetyl salicylic acid at 3.05 A resolution | ||||||
Components | Chitinase-3-like protein 1 | ||||||
Keywords | SIGNALING PROTEIN / SPB-40 / TIM barrel / N-acetyl salicylic acid / Signalling protein | ||||||
Function / homology | Function and homology information response to interleukin-6 / activation of NF-kappaB-inducing kinase activity / chitin binding / response to tumor necrosis factor / response to mechanical stimulus / response to interleukin-1 / positive regulation of peptidyl-threonine phosphorylation / positive regulation of interleukin-8 production / lung development / positive regulation of angiogenesis ...response to interleukin-6 / activation of NF-kappaB-inducing kinase activity / chitin binding / response to tumor necrosis factor / response to mechanical stimulus / response to interleukin-1 / positive regulation of peptidyl-threonine phosphorylation / positive regulation of interleukin-8 production / lung development / positive regulation of angiogenesis / cellular response to tumor necrosis factor / carbohydrate binding / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / carbohydrate metabolic process / inflammatory response / apoptotic process / perinuclear region of cytoplasm / endoplasmic reticulum / extracellular space / cytoplasm Similarity search - Function | ||||||
Biological species | Bubalus bubalis (water buffalo) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å | ||||||
Authors | Yamini, S. / Chaudhary, A. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P. | ||||||
Citation | Journal: To be Published Title: Crystal structure of the complex of signaling glycoprotein, SPB-40 and N-acetyl salicylic acid at 3.05 A resolution Authors: Yamini, S. / Chaudhary, A. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nsb.cif.gz | 88.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nsb.ent.gz | 65.3 KB | Display | PDB format |
PDBx/mmJSON format | 4nsb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ns/4nsb ftp://data.pdbj.org/pub/pdb/validation_reports/ns/4nsb | HTTPS FTP |
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-Related structure data
Related structure data | 2o9oS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 40942.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bubalus bubalis (water buffalo) / Strain: Bubalus bubalis / References: UniProt: Q7YS85 |
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#2: Sugar | ChemComp-NAG / |
#3: Chemical | ChemComp-AIN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.54 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 25mM Tris, 50mM NaCl, 20% ethanol, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 19, 2013 / Details: MIRROR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 3.05→56.69 Å / Num. obs: 8058 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 17 Å2 / Rsym value: 0.103 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 3.05→3.1 Å / Mean I/σ(I) obs: 3.7 / Rsym value: 0.416 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2O9O Resolution: 3.05→41.71 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 2037236.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 69.7002 Å2 / ksol: 0.463233 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.05→41.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.05→3.24 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
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Xplor file |
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