- PDB-6qmu: A tetrahedral boronic acid diester formed by a non-natural amino ... -
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Basic information
Entry
Database: PDB / ID: 6qmu
Title
A tetrahedral boronic acid diester formed by a non-natural amino acid in the ligand pocket of an engineered lipocalin
Components
Neutrophil gelatinase-associated lipocalin
Keywords
TRANSPORT PROTEIN / BETA-BARREL / P-BORONOPHENYLALANINE / LIPOCALIN / STREP-TAG / SUGAR
Function / homology
Function and homology information
siderophore transport / Metal sequestration by antimicrobial proteins / iron ion sequestering activity / enterobactin binding / Iron uptake and transport / specific granule lumen / positive regulation of cold-induced thermogenesis / Interleukin-4 and Interleukin-13 signaling / defense response to bacterium / iron ion binding ...siderophore transport / Metal sequestration by antimicrobial proteins / iron ion sequestering activity / enterobactin binding / Iron uptake and transport / specific granule lumen / positive regulation of cold-induced thermogenesis / Interleukin-4 and Interleukin-13 signaling / defense response to bacterium / iron ion binding / innate immune response / apoptotic process / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function
Mass: 21870.545 Da / Num. of mol.: 2 / Mutation: L36T2C Y52F K125W K134N Source method: isolated from a genetically manipulated source Details: Residues 179-188 correspond to the Strep-tag, which was used for affinity purification. Source: (gene. exp.) Homo sapiens (human) / Gene: LCN2, HNL, NGAL / Production host: Escherichia coli (E. coli) / References: UniProt: P80188
Resolution: 1.98→66.89 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.886 / WRfactor Rfree: 0.2709 / WRfactor Rwork: 0.2079 / FOM work R set: 0.8275 / SU B: 9.011 / SU ML: 0.126 / SU R Cruickshank DPI: 0.2114 / SU Rfree: 0.1947 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.211 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2705
1283
4.9 %
RANDOM
Rwork
0.2068
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obs
0.2098
25008
97.14 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
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