negative regulation of ERBB signaling pathway / legumain / vacuolar protein processing / renal system process / Vitamin D (calciferol) metabolism / receptor catabolic process / vitamin D metabolic process / self proteolysis / endolysosome lumen / response to acidic pH ...negative regulation of ERBB signaling pathway / legumain / vacuolar protein processing / renal system process / Vitamin D (calciferol) metabolism / receptor catabolic process / vitamin D metabolic process / self proteolysis / endolysosome lumen / response to acidic pH / activation of cysteine-type endopeptidase activity / dendritic spine organization / positive regulation of monocyte chemotaxis / Trafficking and processing of endosomal TLR / positive regulation of endothelial cell chemotaxis / negative regulation of multicellular organism growth / cellular response to hepatocyte growth factor stimulus / associative learning / protein maturation / endopeptidase activator activity / cellular response to calcium ion / MHC class II antigen presentation / positive regulation of mitotic cell cycle / lysosomal lumen / proteolysis involved in protein catabolic process / positive regulation of long-term synaptic potentiation / tau protein binding / memory / cellular response to amyloid-beta / antigen processing and presentation of exogenous peptide antigen via MHC class II / late endosome / apical part of cell / peptidase activity / negative regulation of neuron apoptotic process / lysosome / cysteine-type endopeptidase activity / negative regulation of gene expression / positive regulation of cell population proliferation / perinuclear region of cytoplasm / proteolysis / extracellular exosome / extracellular region / cytoplasm Similarity search - Function
CHAIN I IS A COVALENTLY LINKED TO CHAIN A VIA A CH2 GROUP. CHAIN I IS AN ACTIVE SITE-DIRECTED COVALENT INHIBITOR. THE STRUCTURE THEREFORE PRESENTS AS EFFECTIVELY A MONOMERIC FORM.
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.48 Å3/Da / Density % sol: 49 % Description: AUTO-RICKSHAW WAS USED TO DETERMINE AN INITIAL MODEL OF A MERCURY DERIVATIVE (1.0059) FOLLOWED BY MOLECULAR REPLACEMENT INTO A NATIVE DATASET.
Crystal grow
pH: 7.5 Details: 0.1 M HEPES PH 7.5, 0.2 M LITHIUM SULFATE MONOHYDRATE, 25 % PEG 3350
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.0722 Å / Relative weight: 1
Reflection twin
Crystal-ID
ID
Operator
Domain-ID
Fraction
1
1
H, K, L
1
0.663
1
1
-H, K, -L
2
0.337
Reflection
Resolution: 2.18→49.79 Å / Num. obs: 16856 / % possible obs: 100 % / Redundancy: 14.3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 17.4
Reflection shell
Resolution: 2.18→2.29 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 5.8 / % possible all: 100
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Processing
Software
Name
Version
Classification
REFMAC
5.6.0117
refinement
iMOSFLM
datareduction
SCALA
datascaling
Refinement
Method to determine structure: SIRAS Starting model: NONE Resolution: 2.2→48 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.924 / SU B: 7.269 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.207
815
5.5 %
RANDOM
Rwork
0.18031
-
-
-
obs
0.1817
13893
90.12 %
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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