- PDB-5z3s: Crystal structure of butanol modified signaling protein from buff... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 5z3s
Title
Crystal structure of butanol modified signaling protein from buffalo (SPB-40) at 1.65 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 / chitinase activity / chitin catabolic process / 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 ...response to interleukin-6 / activation of NF-kappaB-inducing kinase activity / chitinase activity / chitin catabolic process / 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 / carbohydrate metabolic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / inflammatory response / apoptotic process / perinuclear region of cytoplasm / endoplasmic reticulum / extracellular space / cytoplasm Similarity search - Function
Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Glycoside hydrolase superfamily Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O
Sequence details
Sequence of this structure is based on reference 1 of database Q7YS85 (CH3L1_BUBBU) in UniProtKB. ...Sequence of this structure is based on reference 1 of database Q7YS85 (CH3L1_BUBBU) in UniProtKB. Residue D232 is missing according to the reference.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.7 Å3/Da / Density % sol: 54.4 %
Resolution: 1.65→56.37 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.559 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.20582
2543
4.8 %
RANDOM
Rwork
0.16495
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obs
0.1669
50253
99.2 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK