- PDB-4i2x: Crystal structure of Signal Regulatory Protein gamma (SIRP-gamma)... -
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Basic information
Entry
Database: PDB / ID: 4i2x
Title
Crystal structure of Signal Regulatory Protein gamma (SIRP-gamma) in complex with FabOX117
Components
FabOX117 heavy chain
FabOX117 light chain
Signal-regulatory protein gamma
Keywords
IMMUNE SYSTEM / Protein-Fab complex / Structural Genomics / Oxford Protein Production Facility / OPPF / Signal Regulatory Protein / CD47 / cell surface
Function / homology
Function and homology information
positive regulation of cell-cell adhesion / Signal regulatory protein family interactions / positive regulation of phagocytosis / Cell surface interactions at the vascular wall / positive regulation of T cell activation / cell-cell signaling / cell adhesion / intracellular signal transduction / negative regulation of cell population proliferation / positive regulation of cell population proliferation ...positive regulation of cell-cell adhesion / Signal regulatory protein family interactions / positive regulation of phagocytosis / Cell surface interactions at the vascular wall / positive regulation of T cell activation / cell-cell signaling / cell adhesion / intracellular signal transduction / negative regulation of cell population proliferation / positive regulation of cell population proliferation / membrane / plasma membrane Similarity search - Function
Resolution: 2.48→29.82 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.909 / SU B: 22.005 / SU ML: 0.231 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.378 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.25996
3594
5.1 %
RANDOM
Rwork
0.19571
-
-
-
obs
0.19891
67546
98.99 %
-
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: 61.151 Å2
Baniso -1
Baniso -2
Baniso -3
1-
2.89 Å2
-0 Å2
-0 Å2
2-
-
0.07 Å2
0 Å2
3-
-
-
-2.96 Å2
Refinement step
Cycle: LAST / Resolution: 2.48→29.82 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
11480
0
31
302
11813
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.006
0.019
11813
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.147
1.944
16112
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.053
5
1477
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.755
24.083
480
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.359
15
1879
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
13.617
15
55
X-RAY DIFFRACTION
r_chiral_restr
0.073
0.2
1824
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.021
8907
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
X-RAY DIFFRACTION
r_scbond_it
X-RAY DIFFRACTION
r_scangle_it
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.479→2.543 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.393
250
-
Rwork
0.348
4336
-
obs
-
-
87.75 %
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
1.4524
0.4918
0.238
2.2918
0.9276
2.0167
-0.1183
0.0374
-0.0292
-0.0929
0.2958
-0.3167
-0.2236
0.3439
-0.1775
0.0521
-0.004
-0.0225
0.14
-0.0697
0.1998
29.72
42.515
18.057
2
0.7516
0.3333
-0.952
1.0238
0.6341
5.12
0.0423
-0.304
0.0399
0.4094
0.1371
-0.3903
-0.1637
0.2279
-0.1794
0.3195
0.1947
-0.2685
0.3146
-0.1914
0.3078
35.496
54.053
53.557
3
0.9446
-0.3348
-0.1627
2.3081
1.479
3.1245
0.0329
-0.0511
0.0277
0.155
-0.0513
0.1167
0.0682
-0.2423
0.0184
0.0616
0.0351
-0.0313
0.0815
0.0054
0.1449
9.029
40.169
25.198
4
0.9759
1.5349
0.7692
2.5172
1.2957
2.9849
0.1154
-0.0826
0.1151
0.2785
0.0637
0.0209
0.0758
0.1745
-0.1791
0.2713
0.1698
-0.2002
0.3699
-0.2243
0.4033
22.816
61.023
50.921
5
2.0435
1.3157
-1.6803
2.3648
-0.8117
2.4268
0.1108
-0.2234
0.2526
-0.0061
0.0719
0.1141
-0.1202
0.123
-0.1827
0.0111
-0.032
0.019
0.1888
-0.0769
0.1922
48.596
25.609
-5.449
6
1.9207
0.9969
0.6635
2.1767
0.165
3.3099
-0.3474
0.4168
0.5032
-0.781
0.2371
0.5064
-0.0032
-0.4978
0.1103
0.2976
-0.1294
-0.1514
0.3367
0.1001
0.2729
55.045
32.773
-41.832
7
1.5619
0.5169
-1.0681
1.2303
-0.3332
3.0514
-0.3087
-0.0761
-0.2586
-0.0684
0.2225
-0.1179
0.3445
0.218
0.0862
0.0797
0.0384
0.0107
0.1527
-0.0138
0.1643
48.747
4.728
-12.35
8
4.1684
3.2675
-0.6672
3.9309
-0.4958
1.4244
-0.3503
0.2548
-0.0218
-0.4425
0.2702
-0.1996
0.3772
-0.0257
0.0801
0.1803
-0.1281
0.0541
0.2333
-0.0585
0.1133
63.751
20.622
-37.568
9
1.5168
-0.673
-0.131
3.4754
-0.084
2.2638
0.0735
0.4835
-0.0614
-0.4189
-0.1479
0.3013
-0.255
-0.4113
0.0744
0.1118
0.0868
-0.0921
0.3044
-0.0447
0.1169
4.39
32.058
0.502
10
0.4206
-0.4273
0.4456
1.3015
-0.6516
2.7177
-0.0041
-0.0163
-0.0405
0.1862
-0.038
0.0065
-0.1533
0.082
0.0421
0.1745
0.0221
-0.03
0.1246
-0.015
0.0698
24.635
9.451
30.742
11
2.7979
-0.9559
0.8954
5.8129
-1.9977
1.66
-0.137
-0.6454
-0.3791
1.0408
0.2676
0.333
-0.0878
0.0141
-0.1305
0.6077
0.1115
0.0692
0.295
0.1016
0.2211
24.995
-13.498
62.496
12
2.5469
-0.6681
-0.0571
2.3798
-0.7723
2.5008
0.005
-0.4653
-0.2266
0.4736
-0.0519
-0.2348
0.2753
0.4303
0.0469
0.2608
0.0971
-0.0416
0.3366
0.1092
0.1279
43.16
-0.669
12.844
13
1.3829
-0.1994
0.5259
0.2223
-0.1585
5.8606
0.0215
0.1278
0.1235
-0.2366
-0.0416
0.0156
-0.2236
-0.4209
0.0201
0.3085
0.0643
-0.0023
0.1983
0.0236
0.1949
17.059
15.613
-16.753
14
8.18
0.0783
4.3686
3.6236
3.8091
7.5626
0.3158
0.8124
-0.5941
-0.8523
-0.8212
1.3779
-0.1884
-1.7822
0.5054
1.1835
0.0461
-0.4268
1.9998
0.145
1.1635
-6.362
11.777
-48.08
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
1 - 108
2
X-RAY DIFFRACTION
2
A
109 - 214
3
X-RAY DIFFRACTION
3
B
1 - 119
4
X-RAY DIFFRACTION
4
B
120 - 229
5
X-RAY DIFFRACTION
5
C
1 - 108
6
X-RAY DIFFRACTION
6
C
109 - 214
7
X-RAY DIFFRACTION
7
D
1 - 119
8
X-RAY DIFFRACTION
8
D
120 - 219
9
X-RAY DIFFRACTION
9
E
2 - 115
10
X-RAY DIFFRACTION
10
E
116 - 221
11
X-RAY DIFFRACTION
11
E
222 - 317
12
X-RAY DIFFRACTION
12
F
2 - 115
13
X-RAY DIFFRACTION
13
F
116 - 221
14
X-RAY DIFFRACTION
14
F
222 - 315
+
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