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Yorodumi- PDB-1zl1: Crystal structure of the complex of signalling protein from sheep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zl1 | |||||||||
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Title | Crystal structure of the complex of signalling protein from sheep (SPS-40) with a designed peptide Trp-His-Trp reveals significance of Asn79 and Trp191 in the complex formation | |||||||||
Components |
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Keywords | SIGNALING PROTEIN / SIGNALLING PROTEIN / COMPLEX TRP-HIS-TRP | |||||||||
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 | Ovis aries (sheep) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | |||||||||
Authors | Ethayathulla, A.S. / Srivastava, D.B. / Singh, N. / Kumar, J. / Somvanshi, R.K. / Sharma, S. / Dey, S. / Singh, T.P. | |||||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of the complex of signalling protein from sheep (SPS-40) with a designed peptide Trp-His-Trp reveals significance of Asn79 and Trp191 in the complex formation Authors: Ethayathulla, A.S. / Srivastava, D.B. / Singh, N. / Kumar, J. / Somvanshi, R.K. / Sharma, S. / Dey, 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 | 1zl1.cif.gz | 88.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zl1.ent.gz | 65.6 KB | Display | PDB format |
PDBx/mmJSON format | 1zl1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/1zl1 ftp://data.pdbj.org/pub/pdb/validation_reports/zl/1zl1 | HTTPS FTP |
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-Related structure data
Related structure data | 1r2v 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: 40612.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: Q6TMG6 |
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#2: Protein/peptide | Mass: 528.582 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Trp-His-Trp SOLID PHASE PEPTIDE SYNTHESIS |
#3: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#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: 2.8 Å3/Da / Density % sol: 56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 25mM tris HCl,50mM NaCl, 11% ethanol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 4, 2004 / Details: MIRROR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→56 Å / Num. obs: 5105 / % possible obs: 89.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 35 Å2 / Rsym value: 0.2 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 3.5→3.56 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.59 / % possible all: 85.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1r2v 1r2v Resolution: 3.5→56 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.874 / SU B: 35.985 / SU ML: 0.593 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.62 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 25.56 Å2
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Refinement step | Cycle: LAST / Resolution: 3.5→56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.5→3.588 Å / Total num. of bins used: 20 /
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