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Yorodumi- PDB-5z05: Crystal structure of signalling protein from buffalo (SPB-40) wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5z05 | ||||||||||||
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Title | Crystal structure of signalling protein from buffalo (SPB-40) with an acetone induced conformation of Trp78 at 1.49 A resolution | ||||||||||||
Components | Chitinase-3-like protein 1 | ||||||||||||
Keywords | SIGNALING 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: 1.49 Å | ||||||||||||
Authors | Singh, P.K. / Chaudhary, A. / Tyagi, T.K. / Kaur, P. / Sharma, S. / Singh, T.P. | ||||||||||||
Citation | Journal: Arch. Biochem. Biophys. / Year: 2018 Title: A glycoprotein from mammary gland secreted during involution promotes apoptosis: Structural and biological studies Authors: Chaudhary, A. / Kumar, V. / Singh, P.K. / Sharma, P. / Bairagya, H.R. / Kaur, P. / Sharma, S. / Chauhan, S.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 | 5z05.cif.gz | 181.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z05.ent.gz | 141.4 KB | Display | PDB format |
PDBx/mmJSON format | 5z05.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z0/5z05 ftp://data.pdbj.org/pub/pdb/validation_reports/z0/5z05 | HTTPS FTP |
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-Related structure data
Related structure data | 5z3sC 5z4wC 5wsi S: Starting model for refinement C: citing same article (ref.) |
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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: 40710.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bubalus bubalis (water buffalo) / References: UniProt: Q7YS85 |
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#2: Polysaccharide | 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: Chemical | ChemComp-MPD / ( |
#4: Chemical | ChemComp-ACN / |
#5: 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: 2.62 Å3/Da / Density % sol: 52.96 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 35mM Tris -HCl pH- 8.0, 25mM Nacl, 20% Acetone. / PH range: 5-8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 2, 2014 / 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: 1.49→56.32 Å / Num. obs: 65450 / % possible obs: 99 % / Redundancy: 4.2 % / Biso Wilson estimate: 20.4 Å2 / Rsym value: 0.03 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.49→1.53 Å / Mean I/σ(I) obs: 2.2 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WSI 5wsi Resolution: 1.49→56.32 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.435 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.061 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.13 Å2
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Refinement step | Cycle: 1 / Resolution: 1.49→56.32 Å
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Refine LS restraints |
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