Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE THE EXPERIMENTAL INFO OF UNIPROT (Q8AYA3, AGGB2_AGKAC) SHOWS CONFLICT AT THIS POSITION: A -> S ...THE THE EXPERIMENTAL INFO OF UNIPROT (Q8AYA3, AGGB2_AGKAC) SHOWS CONFLICT AT THIS POSITION: A -> S (IN REF.1; AAL66390).
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.1 Å3/Da / Density % sol: 41.5 %
Crystal grow
Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.28M ammonium sulfate, 17.6% PEG 8000, 0.2M lithium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9791 Å / Relative weight: 1
Reflection
Resolution: 1.91→50 Å / Num. obs: 18923 / % possible obs: 93.9 %
-
Processing
Software
Name
Version
Classification
HKL-2000
datacollection
MOLREP
phasing
REFMAC
5.5.0109
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 10.297 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22239
974
5.2 %
RANDOM
Rwork
0.19171
-
-
-
obs
0.1933
17895
93.58 %
-
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: 41.609 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.34 Å2
0 Å2
0 Å2
2-
-
2.84 Å2
0 Å2
3-
-
-
-2.5 Å2
Refinement step
Cycle: LAST / Resolution: 1.91→50 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2081
0
23
135
2239
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.013
0.022
2162
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.355
1.936
2921
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.669
5
254
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.168
24.51
102
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.54
15
375
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
22.443
15
8
X-RAY DIFFRACTION
r_chiral_restr
0.095
0.2
294
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
1623
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
0.732
1.5
1269
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.29
2
2036
X-RAY DIFFRACTION
r_scbond_it
2.027
3
893
X-RAY DIFFRACTION
r_scangle_it
3.03
4.5
885
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.915→1.965 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.296
61
-
Rwork
0.378
1016
-
obs
-
-
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
6.0067
4.74
-6.0895
21.1565
-6.98
4.5043
-0.1271
-1.2393
0.199
1.2697
0.2466
-0.3641
-0.0754
0.6733
-0.1195
0.3913
-0.0352
-0.0213
0.5398
-0.0558
0.0542
21.487
-5.019
-0.399
2
3.6542
-1.7897
3.318
3.3984
0.1575
4.7947
-0.0316
-0.2796
-0.0603
0.3386
0.1953
-0.0742
0.0378
0.3717
-0.1637
0.2508
-0.0496
-0.006
0.3884
-0.0012
0.1201
22.531
-7.275
-7.244
3
6.9098
1.2456
1.2475
2.0651
0.75
3.9041
-0.1217
-0.1371
0.1825
0.246
-0.0956
0.2253
-0.501
-0.1344
0.2173
0.279
-0.0381
0.0236
0.2186
-0.0133
0.2143
9.412
-0.113
-14.154
4
2.2252
-0.0079
-0.3094
4.3358
5.5928
10.8554
-0.1073
-0.0719
0.0958
0.4158
-0.1045
0.1327
-0.2395
0.1642
0.2118
0.3571
-0.1233
-0.0045
0.2994
0.014
0.1649
18.45
2.137
-9.772
5
4.8546
-0.5609
-1.8723
1.6093
-0.6559
5.3501
0.1183
-0.1509
-0.0968
0.228
0.0783
-0.0367
0.4466
0.8364
-0.1967
0.2153
0.0306
-0.0376
0.4211
-0.0364
0.1895
24.15
-12.874
-14.971
6
28.7762
3.6635
3.1274
8.4051
2.9829
22.1658
0.5021
-1.4982
-0.7129
0.4887
0.1338
0.3435
0.5193
-0.105
-0.6359
0.2871
-0.051
0.0476
0.2326
0.0879
0.2164
12.743
-16.916
-9.449
7
9.0765
8.3277
3.2534
11.2146
1.62
4.0962
0.1897
-0.468
-0.2554
-0.0103
-0.2157
0.0531
-0.2003
0.3102
0.026
0.1899
-0.0389
0.013
0.2716
0.0165
0.2096
10.719
-9.686
-18.637
8
5.7996
-0.0084
5.7096
0.2714
-1.778
8.2677
-0.3029
0.2096
0.2275
0.1922
0.0526
0.0836
-0.7943
0.8119
0.2503
0.2798
-0.1733
-0.0098
0.3548
0.0066
0.1622
15.156
2.385
-33.632
9
6.1292
-0.1075
-0.4962
4.22
2.6377
12.3763
0.2499
-0.0804
0.0751
-0.2502
-0.1741
-0.1846
-0.1954
0.4241
-0.0757
0.1716
-0.0014
0.0539
0.3068
0.001
0.1701
13.487
0.648
-49.687
10
-1.3114
1.4236
-1.5954
7.3923
-6.2913
9.8418
0.1871
-0.164
0.1177
0.3477
-0.0644
0.2857
-0.099
0.0293
-0.1228
0.1907
-0.0676
0.0496
0.4263
-0.0557
0.1799
4.288
0.667
-35.877
11
2.5559
2.3562
-0.2887
4.9644
-4.5884
6.2115
-0.222
0.2947
0.0258
-0.1439
0.2636
0.1558
-0.0657
0.2395
-0.0417
0.1911
-0.0828
-0.0188
0.355
0.0277
0.1653
13.207
-7.087
-25.933
12
3.4666
-0.0264
-0.1094
5.6096
-2.0495
5.587
0.0069
0.2731
-0.4344
-0.1927
0.1987
0.1303
0.4253
0.3499
-0.2056
0.2003
-0.0272
-0.0101
0.3139
-0.051
0.2225
15.591
-13.987
-22.962
13
6.7222
0.8057
4.9816
0.8675
1.0038
5.8248
-0.023
-0.1153
0.1051
0.0816
-0.0146
0.0852
-0.1131
0.0884
0.0376
0.2324
-0.0628
0.023
0.281
0.0047
0.1974
13.065
-3.735
-14.971
14
0.6065
-1.6193
3.359
9.8653
-6.8891
10.159
-0.0413
0.6039
0.0417
-1.0776
-0.1558
0.0736
1.3006
0.6135
0.1972
0.4908
0.0452
-0.1082
0.42
-0.0645
0.1663
0.769
-3.576
-67.338
15
2.7738
-0.3746
0.5306
4.987
-1.1659
2.3297
0.1069
0.1375
-0.1649
-0.4747
-0.0638
0.1719
0.1175
0.0476
-0.0431
0.2296
0.0008
-0.0308
0.2114
-0.0829
0.157
1.82
-6.604
-55.374
16
5.1908
2.5895
-6.1552
1.4269
-2.9435
11.306
0.1114
0.2517
-0.4896
-0.3753
-0.0133
-0.6593
0.8102
0.6018
-0.0981
0.3992
0.1523
0.0053
0.2565
-0.1414
0.3275
9.941
-14.032
-54.853
17
3.4178
1.9644
0.5671
5.386
2.2663
6.306
-0.011
0.4961
-0.2679
-0.5206
0.0123
-0.2191
0.2397
0.5389
-0.0013
0.3192
0.0805
0.0434
0.3451
-0.0745
0.1684
8.996
-6.987
-58.784
18
3.3517
1.8849
0.2349
6.5433
-0.9391
1.7537
0.2217
-0.1108
0.3136
0.0994
-0.174
0.8219
0.0006
-0.1096
-0.0477
0.1583
-0.0173
0.0399
0.2629
-0.1155
0.2879
-4.541
-1.378
-49.866
19
3.5452
2.703
3.1577
3.8808
2.7401
6.9261
0.381
-0.0752
-0.4135
0.0479
-0.1177
-0.2087
0.1262
0.6889
-0.2633
0.2321
-0.0483
-0.0092
0.3491
-0.0144
0.2065
11.33
-5.931
-41.985
20
5.3388
-4.7814
4.6615
10.0876
0.8921
30.6131
0.5744
0.4798
-0.0759
-0.2497
-0.3002
-0.1948
-1.3034
1.6302
-0.2742
0.133
-0.2604
-0.0264
0.5761
0.0873
0.0728
21.971
-0.339
-27.815
21
5.1464
-2.4443
-0.8243
13.2499
2.2674
3.6666
0.2974
0.399
0.0472
-0.1636
-0.2394
-0.5342
-0.4018
1.1764
-0.058
0.1426
-0.1832
-0.0324
0.701
0.0467
0.0384
26.619
-3.543
-23.146
22
22.0322
-5.1265
45.8592
-2.2184
-0.767
80.3724
1.1967
0.155
-2.1129
-0.7607
1.1436
0.6099
1.6785
1.7735
-2.3403
0.319
-0.0117
-0.0813
0.6386
0.0108
0.3971
16.989
-12.344
-33.229
23
7.8923
-3.7584
15.1121
8.0833
-5.2944
7.8384
0.5825
-1.3115
-0.0249
-0.0761
-0.2794
0.7142
0.4652
-0.7642
-0.3032
0.2159
-0.1287
0.0707
0.5596
-0.1313
0.2342
0.084
-5.841
-43.255
24
4.299
-2.7056
2.3418
8.6866
-1.0636
5.1302
0.1889
-1.0029
0.2855
0.7972
-0.1841
0.9486
0.0165
-0.3563
-0.0048
0.1952
-0.1747
0.0839
0.4962
-0.1441
0.2906
1.549
-3.175
-40.716
25
2.573
2.6292
-0.7407
4.6066
-1.446
8.027
0.5332
-0.4153
-0.3246
-0.0384
-0.4512
0.0624
0.7617
0.1231
-0.082
0.3457
-0.0084
-0.0361
0.2295
-0.0171
0.2592
3.559
-15.059
-45.884
26
8.0863
-1.4381
5.0582
2.3693
0.4985
2.637
-0.3642
0.4871
0.3507
-0.6191
0.0818
0.0941
0.0335
0.7568
0.2824
0.4278
0.0221
0.0534
0.3899
-0.0595
0.1273
7.058
-1.561
-61.159
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
2 - 8
2
X-RAY DIFFRACTION
2
A
9 - 19
3
X-RAY DIFFRACTION
3
A
20 - 32
4
X-RAY DIFFRACTION
4
A
33 - 43
5
X-RAY DIFFRACTION
5
A
44 - 57
6
X-RAY DIFFRACTION
6
A
58 - 62
7
X-RAY DIFFRACTION
7
A
63 - 69
8
X-RAY DIFFRACTION
8
A
70 - 80
9
X-RAY DIFFRACTION
9
A
81 - 90
10
X-RAY DIFFRACTION
10
A
91 - 99
11
X-RAY DIFFRACTION
11
A
100 - 106
12
X-RAY DIFFRACTION
12
A
107 - 117
13
X-RAY DIFFRACTION
13
A
118 - 131
14
X-RAY DIFFRACTION
14
B
1 - 9
15
X-RAY DIFFRACTION
15
B
10 - 25
16
X-RAY DIFFRACTION
16
B
26 - 33
17
X-RAY DIFFRACTION
17
B
34 - 44
18
X-RAY DIFFRACTION
18
B
45 - 65
19
X-RAY DIFFRACTION
19
B
66 - 76
20
X-RAY DIFFRACTION
20
B
77 - 81
21
X-RAY DIFFRACTION
21
B
82 - 91
22
X-RAY DIFFRACTION
22
B
92 - 97
23
X-RAY DIFFRACTION
23
B
98 - 104
24
X-RAY DIFFRACTION
24
B
105 - 112
25
X-RAY DIFFRACTION
25
B
113 - 121
26
X-RAY DIFFRACTION
26
B
122 - 126
+
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