positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function
Resolution: 1.8→23.95 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.912 / SU B: 6.437 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.362 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2405
522
5.2 %
RANDOM
Rwork
0.18437
-
-
-
obs
0.18741
9521
98.67 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 10.76 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.01 Å2
0 Å2
-0.01 Å2
2-
-
0 Å2
0 Å2
3-
-
-
-0.01 Å2
Refinement step
Cycle: LAST / Resolution: 1.8→23.95 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
840
0
0
124
964
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.018
0.022
862
X-RAY DIFFRACTION
r_bond_other_d
0.003
0.02
594
X-RAY DIFFRACTION
r_angle_refined_deg
1.694
1.95
1173
X-RAY DIFFRACTION
r_angle_other_deg
2.015
3
1448
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.485
5
105
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.515
23.953
43
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.251
15
152
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.651
15
5
X-RAY DIFFRACTION
r_chiral_restr
0.1
0.2
126
X-RAY DIFFRACTION
r_gen_planes_refined
0.009
0.021
953
X-RAY DIFFRACTION
r_gen_planes_other
0.003
0.02
179
X-RAY DIFFRACTION
r_mcbond_it
1.214
1.5
511
X-RAY DIFFRACTION
r_mcbond_other
0.452
1.5
200
X-RAY DIFFRACTION
r_mcangle_it
1.906
2
839
X-RAY DIFFRACTION
r_scbond_it
2.902
3
351
X-RAY DIFFRACTION
r_scangle_it
4.222
4.5
331
X-RAY DIFFRACTION
r_rigid_bond_restr
1.484
3
1456
X-RAY DIFFRACTION
r_sphericity_free
6.631
3
128
X-RAY DIFFRACTION
r_sphericity_bonded
1.93
3
1430
LS refinement shell
Resolution: 1.8→1.847 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.271
33
-
Rwork
0.182
697
-
obs
-
-
99.32 %
+
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