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Yorodumi- PDB-1zbw: Crystal structure of the complex formed between signalling protei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zbw | ||||||
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Title | Crystal structure of the complex formed between signalling protein from goat mammary gland (SPG-40) and a tripeptide Trp-Pro-Trp at 2.8A resolution | ||||||
Components |
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Keywords | SIGNALLING PROTEIN / ligand / wpw / 2.8A | ||||||
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: 2.8 Å | ||||||
Authors | Kumar, J. / Ethayathulla, A.S. / Srivastava, D.B. / Singh, N. / Sharma, S. / Somvanshi, R.K. / Dey, S. / Singh, T.P. | ||||||
Citation | Journal: to be published Title: Crystal structure of the complex formed between signalling protein from goat mammary gland (SPG-40) and a tripeptide Trp-Pro-Trp at 2.8A resolution Authors: Kumar, J. / Ethayathulla, A.S. / Srivastava, D.B. / Singh, N. / Sharma, S. / Somvanshi, R.K. / 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 | 1zbw.cif.gz | 88.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zbw.ent.gz | 66.5 KB | Display | PDB format |
PDBx/mmJSON format | 1zbw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/1zbw ftp://data.pdbj.org/pub/pdb/validation_reports/zb/1zbw | HTTPS FTP |
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-Related structure data
Related structure data | 1sytS 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: 40728.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Capra hircus (goat) / References: UniProt: Q8SPQ0 | ||
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#2: Protein/peptide | Mass: 487.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Trp-Pro-Trp solid phase peptide synthesis | ||
#3: Sugar | #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, 19% 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: Oct 26, 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: 2.8→56 Å / Num. all: 11400 / Num. obs: 11373 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 36 Å2 / Rsym value: 0.136 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.8→2.85 Å / Mean I/σ(I) obs: 2.9 / Rsym value: 0.53 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1syt Resolution: 2.8→56 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.924 / SU B: 15.562 / SU ML: 0.316 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.309 / 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: 32.593 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 Å / Total num. of bins used: 20 /
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