regulation of B cell cytokine production / proteoglycan catabolic process / monocyte proliferation / positive regulation of interleukin-17A production / regulation of B cell apoptotic process / eosinophil homeostasis / positive regulation of type III hypersensitivity / B cell affinity maturation / positive regulation of synoviocyte proliferation / histamine secretion by mast cell ...regulation of B cell cytokine production / proteoglycan catabolic process / monocyte proliferation / positive regulation of interleukin-17A production / regulation of B cell apoptotic process / eosinophil homeostasis / positive regulation of type III hypersensitivity / B cell affinity maturation / positive regulation of synoviocyte proliferation / histamine secretion by mast cell / neutrophil homeostasis / cellular response to molecule of fungal origin / positive regulation of type I hypersensitivity / cellular response to interleukin-7 / MyD88 deficiency (TLR2/4) / MyD88-dependent toll-like receptor signaling pathway / IRAK4 deficiency (TLR2/4) / positive regulation of immunoglobulin production / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / positive regulation of B cell differentiation / positive regulation of NLRP3 inflammasome complex assembly / phospholipase activator activity / negative regulation of interleukin-10 production / B cell activation / negative regulation of B cell proliferation / Fc-epsilon receptor signaling pathway / mesoderm development / phosphatidylinositol-3,4,5-trisphosphate binding / phospholipase binding / RHO GTPases Activate WASPs and WAVEs / positive regulation of B cell proliferation / positive regulation of phagocytosis / cell maturation / FCERI mediated Ca+2 mobilization / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / calcium-mediated signaling / apoptotic signaling pathway / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Regulation of actin dynamics for phagocytic cup formation / G beta:gamma signalling through BTK / cellular response to reactive oxygen species / peptidyl-tyrosine phosphorylation / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / G alpha (12/13) signalling events / DAP12 signaling / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / ER-Phagosome pathway / cytoplasmic vesicle / G alpha (q) signalling events / protein tyrosine kinase activity / adaptive immune response / Potential therapeutics for SARS / response to lipopolysaccharide / intracellular signal transduction / membrane raft / protein phosphorylation / innate immune response / perinuclear region of cytoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal grow
Temperature: 286 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 1 uL protein solution (8.1 mg/mL in 10 mM Tris pH 8.5, 100 mM NaCl, 0.5 mM TCEP, 1 mM GDC0834) and 1 uL reservoir solution of 14% PEG 4000, 0.2 M Ammonium Sulfate, 0.1 M Na Acetate-Acetate ...Details: 1 uL protein solution (8.1 mg/mL in 10 mM Tris pH 8.5, 100 mM NaCl, 0.5 mM TCEP, 1 mM GDC0834) and 1 uL reservoir solution of 14% PEG 4000, 0.2 M Ammonium Sulfate, 0.1 M Na Acetate-Acetate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 286K
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Data collection
Diffraction
Mean temperature: 100 K
Diffraction source
Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97787 Å
Resolution: 1.95→46.98 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.778 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.20251
1053
5 %
RANDOM
Rwork
0.16533
-
-
-
obs
0.16721
20861
99.65 %
-
all
-
20861
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 21.566 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.32 Å2
0.16 Å2
-0 Å2
2-
-
0.32 Å2
-0 Å2
3-
-
-
-0.48 Å2
Refinement step
Cycle: LAST / Resolution: 1.95→46.98 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2158
0
58
182
2398
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.008
0.02
2286
X-RAY DIFFRACTION
r_angle_refined_deg
1.464
1.993
3095
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.781
5
270
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
29.449
24.057
106
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.579
15
417
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.351
15
13
X-RAY DIFFRACTION
r_chiral_restr
0.149
0.2
326
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.021
1724
LS refinement shell
Resolution: 1.952→1.992 Å / Total num. of bins used: 25
Rfactor
Num. reflection
% reflection
Rfree
0.255
70
-
Rwork
0.199
1121
-
obs
-
-
100 %
Refinement TLS params.
Method: refined / Origin x: -35.2128 Å / Origin y: 20.9985 Å / Origin z: -0.6087 Å
11
12
13
21
22
23
31
32
33
T
0.0208 Å2
0.0042 Å2
0.0053 Å2
-
0.0115 Å2
0.0017 Å2
-
-
0.0032 Å2
L
0.4079 °2
0.1513 °2
-0.0331 °2
-
0.7043 °2
-0.2076 °2
-
-
0.4729 °2
S
-0.0172 Å °
-0.0526 Å °
0.0099 Å °
0.0538 Å °
-0.0068 Å °
0.02 Å °
0.0155 Å °
0.0403 Å °
0.0241 Å °
+
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