One biological assembly consisting of one IgE-Fc and two E2_79 is observed in an asymmetric unit.
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Components
#1: Protein
ANTI-IGEINHIBITORE2_79
Mass: 14647.336 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: L7MTK7*PLUS
#2: Protein
IgepsilonchainCregion
Mass: 25637.812 Da / Num. of mol.: 2 / Fragment: IG-LIKE DOMAINS 3 AND 4, RESIDUES 210-428 / Mutation: G216C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGHE / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P01854
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 3.25 Å3/Da / Density % sol: 62.19 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1 M Phosphate-citrate pH 4.2, 5% (w/v) PEG-3000, 25% (v/v) 1,2-propanediol, 10% (v/v) glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
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Data collection
Diffraction
Mean temperature: 100 K
Diffraction source
Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.24→29.753 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.887 / SU ML: 1.43 / σ(F): 1.96 / Phase error: 40.07 / Stereochemistry target values: ML Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE NATIVE DATA WERE SUBMITTED TO THE DIFFRACTION ANISOTROPY SERVER, WHICH INDICATED SIGNIFICANT ANISOTROPY WITH PRINCIPLE COMPONENTS OF 20. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE NATIVE DATA WERE SUBMITTED TO THE DIFFRACTION ANISOTROPY SERVER, WHICH INDICATED SIGNIFICANT ANISOTROPY WITH PRINCIPLE COMPONENTS OF 20.6 X 20.5 X -41.2 (ANGSTROM2) ALONG THE A*. B* AND C* AXES. THE DATA WERE TRUNCATED TO 4.2 ANGSTROM ALONG THE C* AXIS AND 4.5 ANGSTROM ALONG THE A*/B* AXES.
Rfactor
Num. reflection
% reflection
Rfree
0.3378
303
4.74 %
Rwork
0.2704
-
-
obs
0.2734
6399
89.17 %
all
-
9512
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Solvent computation
Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 225.985 Å2 / ksol: 0.327 e/Å3
Displacement parameters
Baniso -1
Baniso -2
Baniso -3
1-
7.63 Å2
0 Å2
-0 Å2
2-
-
7.63 Å2
0 Å2
3-
-
-
-13.7428 Å2
Refinement step
Cycle: LAST / Resolution: 4.24→29.753 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5154
0
0
0
5154
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.012
5273
X-RAY DIFFRACTION
f_angle_d
1.397
7183
X-RAY DIFFRACTION
f_dihedral_angle_d
16.119
1898
X-RAY DIFFRACTION
f_chiral_restr
0.081
823
X-RAY DIFFRACTION
f_plane_restr
0.006
942
Refine LS restraints NCS
Ens-ID
Dom-ID
Auth asym-ID
Number
Refine-ID
Type
Rms dev position (Å)
1
1
C
1629
X-RAY DIFFRACTION
POSITIONAL
1
2
D
1629
X-RAY DIFFRACTION
POSITIONAL
0.272
2
1
A
891
X-RAY DIFFRACTION
POSITIONAL
2
2
B
891
X-RAY DIFFRACTION
POSITIONAL
0.001
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
4.2404-5.3375
0.3748
147
0.303
2699
X-RAY DIFFRACTION
79
5.3375-29.7541
0.3249
156
0.2603
3397
X-RAY DIFFRACTION
99
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
2.1177
-6.7015
-4.7877
4.0326
-0.1288
2.0065
0.6931
-3.2331
-4.8446
2.1986
-3.4938
1.7911
2.9223
1.3135
-3.0571
3.455
-0.6344
0.562
1.1846
-0.468
2.6064
-3.6037
7.4162
-29.0708
2
5.9186
0.6389
-3.8963
-0.1218
-0.7265
4.9981
0.0621
-1.7918
3.0425
-0.8141
0.2347
1.5731
-0.8479
2.9487
0
2.2217
-0.2617
-0.0067
2.0206
-0.5245
2.1918
-9.555
7.538
-30.0495
3
1.4458
-2.6975
-0.5262
4.6409
-0.1741
-0.2288
1.3948
1.0033
-2.3128
3.4554
-3.3505
-2.7181
1.1203
-5.6867
0.067
2.357
-0.8683
-0.8283
1.8479
-0.9545
2.0446
-18.4471
6.7199
-26.5684
4
2.0206
-1.9822
-1.213
1.1852
1.1872
1.0581
-0.2244
3.1847
1.3951
-2.0895
0.9156
-2.5925
2.7885
-2.9196
0.0235
2.4735
-0.7293
0.0222
3.2088
-0.2989
3.5034
-27.1861
2.0576
-22.9586
5
0.3683
-0.3989
0.2916
0.2359
-0.3592
0.4426
2.6416
-4.646
-0.6393
2.4494
4.8636
1.7995
4.278
-0.7748
0.0895
6.6939
-1.4464
0.5277
3.8464
-0.9808
3.3565
-33.5345
8.1131
-17.4755
6
4.1297
6.7358
-4.7763
1.9001
2.0452
9.2701
3.8602
1.077
-2.2311
1.968
-1.2506
2.0397
1.1411
2.5688
-0.2963
3.4408
1.471
-0.4627
1.2311
-0.5178
3.3668
-4.5674
30.2814
32.9824
7
2.1338
-1.3229
2.849
6.6685
-1.4355
2.4505
-2.2416
-0.5972
2.103
-1.3217
-0.874
-1.5861
-0.3256
-0.6414
-0.0203
2.2106
0.4114
0.3411
1.9041
-0.7188
2.6121
-15.1347
35.4407
31.4223
8
3.1558
2.6843
5.3148
3.3255
2.5229
1.9299
3.9207
-5.001
-0.3805
2.0889
1.4082
-1.967
2.1262
-6.7862
0.9935
1.0032
1.1475
0.283
2.0844
-1.281
4.5721
-27.2266
39.1589
26.4735
9
0.8432
-1.4705
1.767
2.8714
-3.4932
3.9131
8.0925
1.5888
2.2497
-2.7409
2.6626
3.832
-1.1029
-2.0159
0.5391
5.6191
0.0914
0.7647
2.807
-0.6626
4.1911
-33.5818
33.0255
21.0858
10
7.4451
-0.0126
2.3599
3.8801
3.9298
2.6979
2.106
1.0967
-0.8658
1.0936
-2.221
0.9564
0.9017
-0.8582
-0.1276
3.0201
0.9316
0.5136
2.2371
0.4609
1.8271
-11.9594
37.3825
5.6445
11
8.5695
1.5552
-6.2471
0.8198
-0.2346
4.6715
-0.3957
1.5306
-0.1117
-0.2428
-0.3615
-0.844
0.0471
-1.2018
-0
2.9307
0.7889
0.3084
1.7793
0.1658
2.4229
-12.4337
38.4966
4.6087
12
0.9729
0.6611
0.6653
5.8317
-4.6578
4.536
0.2885
-0.9177
4.4133
2.4045
0.4514
3.3491
-1.5641
-1.232
0.5533
2.2095
0.5563
1.0354
2.1174
0.7258
3.0289
-13.0237
31.5565
12.3471
13
9.9219
-3.6744
-3.3772
10.686
-1.8221
7.1793
-0.0987
-0.4871
0.9278
0.1565
-0.3485
0.1522
-2.0287
1.1611
-0.0009
1.9588
-0.6112
0.0472
1.9266
0.2732
1.5592
14.365
29.2295
1.5198
14
2.6026
-2.2218
-4.8715
6.8474
0.695
6.007
0.6755
-1.2903
-2.5281
-1.6106
-2.376
4.1733
-2.0385
-0.6797
-0.6089
3.4685
-1.1727
-0.3172
1.8888
0.54
1.0135
-11.8764
3.5478
-2.4465
15
10.1555
2.7761
7.2473
0.2679
3.3862
4.8185
-0.7306
-1.7317
-0.2311
-0.5254
-0.2467
0.6382
-0.2504
-2.691
-0.0004
2.9817
-0.3062
-0.1527
1.8875
0.3002
2.3422
-12.294
2.6879
-1.5235
16
0.9207
-1.285
2.9894
8.9894
-4.9277
7.9694
-0.81
-1.9349
-3.143
-0.4533
0.7454
2.0837
2.2043
-2.469
0.1144
2.6512
-0.6743
-0.4176
2.403
0.5632
2.499
-12.9358
9.8168
-8.7096
17
10.4996
2.4614
5.4291
7.9018
0.4109
3.3015
-0.1125
0.0714
-0.1846
-0.166
-0.3815
-0.1307
2.1899
1.4624
-0.0004
2.1864
0.1979
-0.0094
2.053
0.3133
1.6861
14.3255
11.9503
2.0001
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
chain 'A' and (resseq12:24)
2
X-RAY DIFFRACTION
2
chain 'A' and (resseq25:56)
3
X-RAY DIFFRACTION
3
chain 'A' and (resseq57:92)
4
X-RAY DIFFRACTION
4
chain 'A' and (resseq93:122)
5
X-RAY DIFFRACTION
5
chain 'A' and (resseq123:135)
6
X-RAY DIFFRACTION
6
chain 'B' and (resseq12:32)
7
X-RAY DIFFRACTION
7
chain 'B' and (resseq33:92)
8
X-RAY DIFFRACTION
8
chain 'B' and (resseq93:122)
9
X-RAY DIFFRACTION
9
chain 'B' and (resseq123:135)
10
X-RAY DIFFRACTION
10
chain 'C' and (resseq332:384)
11
X-RAY DIFFRACTION
11
chain 'C' and (resseq385:421)
12
X-RAY DIFFRACTION
12
chain 'C' and (resseq422:443)
13
X-RAY DIFFRACTION
13
chain 'C' and (resseq444:545)
14
X-RAY DIFFRACTION
14
chain 'D' and (resseq333:384)
15
X-RAY DIFFRACTION
15
chain 'D' and (resseq385:421)
16
X-RAY DIFFRACTION
16
chain 'D' and (resseq422:443)
17
X-RAY DIFFRACTION
17
chain 'D' and (resseq444:545)
+
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