- PDB-4r9h: Crystal structure of dimeric S33C beta-2 microglobulin mutant at ... -
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Basic information
Entry
Database: PDB / ID: 4r9h
Title
Crystal structure of dimeric S33C beta-2 microglobulin mutant at 1.9 Angstrom resolution
Components
Beta-2-microglobulin
Keywords
IMMUNE SYSTEM / amyloidosis / protein aggregation / covalent dimer / oligomerization / beta sandwich / inclusion bodies
Function / homology
Function and homology information
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 / DAP12 interactions / negative regulation of receptor binding / 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 / DAP12 interactions / negative regulation of receptor binding / 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 / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / 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 / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / 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 / positive regulation of cellular senescence / peptide antigen binding / 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 / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / 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 / lysosomal membrane / external side of plasma membrane / Golgi 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: 1.9→68.84 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / SU B: 8.457 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.24736
1965
5.1 %
RANDOM
Rwork
0.21179
-
-
-
all
0.21353
39024
-
-
obs
0.21353
36945
99.85 %
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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
Displacement parameters
Biso mean: 42.779 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.18 Å2
0 Å2
0 Å2
2-
-
1.18 Å2
0 Å2
3-
-
-
-2.35 Å2
Refinement step
Cycle: LAST / Resolution: 1.9→68.84 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3297
0
0
168
3465
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.013
0.019
3410
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
3112
X-RAY DIFFRACTION
r_angle_refined_deg
1.402
1.939
4624
X-RAY DIFFRACTION
r_angle_other_deg
2.157
3
7197
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.564
5
394
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.535
24
180
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.672
15
590
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.037
15
20
X-RAY DIFFRACTION
r_chiral_restr
0.111
0.2
481
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.021
3822
X-RAY DIFFRACTION
r_gen_planes_other
0.006
0.02
826
X-RAY DIFFRACTION
r_mcbond_it
3.14
2.849
1582
X-RAY DIFFRACTION
r_mcbond_other
3.14
2.847
1581
X-RAY DIFFRACTION
r_mcangle_it
4.599
4.242
1974
X-RAY DIFFRACTION
r_mcangle_other
4.599
4.245
1975
X-RAY DIFFRACTION
r_scbond_it
4.198
3.409
1828
X-RAY DIFFRACTION
r_scbond_other
4.197
3.411
1829
X-RAY DIFFRACTION
r_scangle_other
6.357
4.899
2651
X-RAY DIFFRACTION
r_long_range_B_refined
8.475
23.82
3643
X-RAY DIFFRACTION
r_long_range_B_other
8.495
23.699
3603
LS refinement shell
Resolution: 1.9→1.949 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.355
140
-
Rwork
0.329
2640
-
obs
-
-
98.9 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
1.2482
0.882
0.1058
0.9859
0.244
0.5216
0.0926
-0.0249
-0.0896
0.0993
-0.0888
-0.1284
0.0975
-0.0501
-0.0039
0.0461
0.0018
-0.0187
0.1041
0.0265
0.0703
6.963
1.0435
15.8611
2
3.2846
0.088
-2.1001
0.5589
-0.0749
1.419
-0.0404
0.2273
-0.0135
0.0751
0.0664
0.0084
0.0428
-0.1278
-0.026
0.0357
0.0546
-0.0019
0.1262
0.0072
0.0673
-23.8634
10.9235
12.9647
3
1.0881
-0.1057
1.5622
0.8864
0.6843
3.3365
-0.1548
-0.0675
-0.0354
-0.2797
0.1536
-0.1117
-0.4693
-0.0157
0.0012
0.2041
0.0028
0.0466
0.0695
-0.0584
0.1056
-36.241
11.098
41.294
4
1.213
-0.4335
0.3867
0.7053
0.9199
2.4742
-0.0478
0.0324
-0.0461
-0.1154
-0.1179
0.1943
-0.1955
-0.216
0.1657
0.1209
0.0204
-0.0571
0.0331
-0.0247
0.1472
14.815
27.993
27.59
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
0 - 99
2
X-RAY DIFFRACTION
2
B
1 - 98
3
X-RAY DIFFRACTION
3
C
1 - 98
4
X-RAY DIFFRACTION
4
D
0 - 97
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