[English] 日本語
Yorodumi- PDB-1syt: Crystal structure of signalling protein from goat SPG-40 in the p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1syt | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of signalling protein from goat SPG-40 in the presense of N,N',N''-triacetyl-chitotriose at 2.6A resolution | |||||||||
Components | BP40 | |||||||||
Keywords | SIGNALING PROTEIN / signalling protein / Goat SPG-40 / 2.6A resolution | |||||||||
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 | Capra hircus (goat) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Kumar, J. / Prem Kumar, R. / Srivastava, D.B. / Sharma, S. / Singh, T.P. | |||||||||
Citation | Journal: to be published Title: Crystal structure of signalling protein from goat SPG-40 in the presense of N,N',N''-triacetyl-chitotriose at 2.6A resolution Authors: Kumar, J. / Prem Kumar, R. / Srivastava, D.B. / Sharma, S. / Singh, T.P. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1syt.cif.gz | 92.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1syt.ent.gz | 68.3 KB | Display | PDB format |
PDBx/mmJSON format | 1syt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sy/1syt ftp://data.pdbj.org/pub/pdb/validation_reports/sy/1syt | HTTPS FTP |
---|
-Related structure data
Related structure data | 1qzo S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological Unit is Monomer |
-Components
#1: Protein | Mass: 40686.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Capra hircus (goat) / References: GenBank: 19526603, UniProt: Q8SPQ0*PLUS |
---|---|
#2: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 25mM Tris-HCl, 50mM NACl, 19% ethanol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5414 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 14, 2004 / Details: MIRROR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5414 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. all: 13563 / Num. obs: 13563 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Rsym value: 0.074 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.6→2.7 Å / Mean I/σ(I) obs: 3.1 / Rsym value: 0.376 / % possible all: 98.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QZO 1qzo Resolution: 2.6→19.8 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 14.361 / SU ML: 0.304 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.313 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.73 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.1921 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→19.8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.718 Å / Total num. of bins used: 20
|