CBS-domain / CBS-domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta / Uncharacterized protein MJ0922
Function and homology information
Biological species
Methanocaldococcus jannaschii DSM 2661 (archaea)
Method
X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.59 Å
Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.23 Å3/Da / Density % sol: 46 %
Crystal grow
Temperature: 289 K / Method: microbatch under oil / pH: 6.3 Details: USING 1.0 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (27.49 mg/ml) AND SOLUTION CONTAINING 27.5% w/v PEG 4000, 0.1 M MES-SODIUM HYDROXIDE, pH 6.3, MICROBATCH UNDER OIL, temperature 289K
Monochromator: SI CHANNEL 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9724 Å / Relative weight: 1
Reflection
Redundancy: 12.6 % / Av σ(I) over netI: 16.7 / Number: 224283 / Rmerge(I) obs: 0.071 / Χ2: 1.65 / D res high: 2.6 Å / D res low: 50 Å / Num. obs: 17759 / % possible obs: 99.4
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
% possible obs (%)
ID
Rmerge(I) obs
Chi squared
Redundancy
5.6
50
98.7
1
0.058
3.156
12.7
4.45
5.6
100
1
0.061
2.707
13.9
3.88
4.45
99.9
1
0.057
2.662
14
3.53
3.88
100
1
0.069
2.078
14
3.28
3.53
100
1
0.083
1.4
13.6
3.08
3.28
100
1
0.106
0.947
13.1
2.93
3.08
100
1
0.16
0.698
12.6
2.8
2.93
99.9
1
0.229
0.597
11.9
2.69
2.8
99.4
1
0.297
0.599
10.8
2.6
2.69
96.3
1
0.382
0.643
9.3
Reflection
Resolution: 2.59→50 Å / Num. obs: 17759 / % possible obs: 99.4 % / Redundancy: 12.6 % / Rsym value: 0.071 / Net I/σ(I): 16.7
Reflection shell
Resolution: 2.59→2.69 Å / Redundancy: 9.3 % / Mean I/σ(I) obs: 4.73 / Rsym value: 0.382 / % possible all: 96.3
-
Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
REFMAC
5.2.0019
refinement
PDB_EXTRACT
2
dataextraction
HKL-2000
datacollection
HKL-2000
datareduction
HKL-2000
datascaling
SGXPRO
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.59→36.47 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.872 / SU B: 30.587 / SU ML: 0.301 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.003 / ESU R Free: 0.37 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.29177
907
5.1 %
RANDOM
Rwork
0.22193
-
-
-
obs
0.22544
17711
99.05 %
-
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: 25.576 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.37 Å2
0 Å2
0 Å2
2-
-
1.87 Å2
0 Å2
3-
-
-
-2.24 Å2
Refinement step
Cycle: LAST / Resolution: 2.59→36.47 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4021
0
0
22
4043
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.013
0.022
3865
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.435
1.967
5251
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.497
5
518
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
39.062
27.424
132
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
17.629
15
676
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
30.953
15
5
X-RAY DIFFRACTION
r_chiral_restr
0.097
0.2
696
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.02
2712
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.229
0.2
1737
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.31
0.2
2787
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.147
0.2
92
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
0.252
0.2
14
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.138
0.2
2
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
0.62
1.5
2641
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
0.945
2
4197
X-RAY DIFFRACTION
r_scbond_it
1.238
3
1350
X-RAY DIFFRACTION
r_scangle_it
1.899
4.5
1050
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.59→2.656 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.456
65
-
Rwork
0.325
1094
-
obs
-
-
90.41 %
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
7.4875
-0.4398
4.6191
1.6503
-5.5031
19.6996
-0.2465
1.6411
-0.1697
-0.5447
-0.7943
0.0323
1.3448
-1.0394
1.0408
0.2634
0.1363
-0.0156
0.3613
0.0655
0.1285
1.7491
60.459
11.7344
2
2.5904
0.194
-1.8484
6.4927
-5.6536
11.4351
0.0775
-0.7095
0.2413
0.9037
0.1466
0.2944
-0.9648
-0.7925
-0.2241
0.359
0.1063
0.0485
0.3375
-0.0099
0.1607
2.9782
59.8173
37.8076
3
9.5939
-3.2016
3.033
5.764
2.0252
4.292
-0.0335
-0.4948
-0.342
0.2296
-0.178
0.2811
-0.7597
-0.4307
0.2114
0.3767
0.0407
-0.012
0.1327
0.0619
0.139
4.6443
52.6596
36.765
4
14.7154
-16.1182
6.3561
25.2308
-4.5737
8.4355
-0.1769
-0.2846
0.8319
-0.1827
0.0993
-0.9238
-0.7276
-0.185
0.0776
0.3686
-0.0497
0.0339
0.1517
-0.0031
0.2104
10.4689
59.9432
36.0384
5
7.5876
-6.9302
4.7219
12.4872
-0.0516
5.8876
-0.5708
-0.7551
0.9638
0.6521
-0.2653
-1.9057
-0.7159
1.5613
0.8361
0.3021
-0.0845
-0.0838
0.5221
0.1336
0.3197
15.2544
58.2848
44.6678
6
7.8204
-0.3834
4.568
8.1275
3.1574
29.732
-0.4422
-0.0485
0.6351
0.1424
-0.5725
-0.2297
-1.5262
0.1203
1.0148
0.2864
-0.0202
-0.0141
-0.0113
0.1029
0.2369
8.1331
65.8705
20.7883
7
26.9319
5.1001
0.4897
9.7846
8.4709
12.5872
0.6284
1.0207
2.5508
-0.9357
-0.5642
0.0128
-0.7092
1.5264
-0.0642
0.2213
-0.0355
0.1936
0.1067
0.2152
0.5083
13.4783
61.55
16.0485
8
3.261
-9.1161
-8.6656
60.2011
17.284
24.415
0.2574
-1.2424
-0.5578
0.6721
0.8344
-2.9919
0.8516
1.8018
-1.0918
0.3582
0.0008
-0.1625
0.3652
0.0086
0.4508
11.9768
58.6513
24.0281
9
7.1185
-5.2804
-3.4443
22.1888
14.2951
20.9543
0.3863
0.4357
0.0283
-0.4537
-0.8091
0.0994
-0.5935
-0.934
0.4228
0.1717
0.0516
-0.029
0.2043
0.0742
0.1435
3.318
59.1977
19.3329
10
4.3526
-0.3549
1.0175
6.6078
-7.2413
18.4868
-0.0541
0.0121
-0.3665
-0.1466
-0.5366
-0.7804
-0.1063
0.8945
0.5907
-0.0565
0.0753
0.0167
0.0778
0.001
0.3498
20.3931
38.8321
21.4758
11
3.0671
-1.8422
-2.5778
5.2423
1.967
3.4976
0.0951
-0.1372
-0.5355
-0.1456
0.1661
-0.0775
0.0026
0.2217
-0.2613
0.2403
-0.0319
-0.0444
0.2251
0.0745
0.2791
15.9894
37.3953
31.2739
12
9.2521
-9.4948
-6.5802
16.0845
5.7529
4.8376
-0.9346
-0.6829
-0.8624
1.7905
0.3131
1.1575
0.5921
-1.0081
0.6215
0.2478
0.0351
0.0062
0.2721
0.1466
0.3865
8.4353
33.0201
39.9167
13
5.6217
-3.6661
0.152
13.9048
-9.022
17.3226
0.4642
0.5785
-0.8432
-1.4115
-0.1767
0.1856
1.3595
-0.9779
-0.2875
0.1213
-0.0127
-0.0648
0.2163
-0.0583
0.2021
13.7725
36.9006
13.6305
14
24.893
0.0414
-27.7912
124.8647
74.6627
75.7265
-0.4567
-0.1145
0.0883
5.6384
-0.3827
4.0379
1.5339
-2.5535
0.8394
0.153
0.0686
0.0318
0.4897
0.335
0.8079
6.5526
41.2236
14.0824
15
27.8486
-24.0965
1.9226
37.5126
-19.8202
19.9172
0.7524
-0.4022
-0.8925
-0.4295
-0.3337
0.0719
-0.6495
-0.3303
-0.4187
-0.1365
-0.1302
-0.0031
0.2992
-0.0156
0.3613
16.31
37.9009
18.2349
16
9.5971
-12.4222
-0.4446
26.668
-7.2845
7.7386
0.5536
0.3255
-0.1054
-0.7641
-0.48
-0.8307
-0.0819
0.0678
-0.0736
0.112
-0.0473
-0.0062
0.2578
0.0523
0.3168
19.1256
44.1519
14.9381
17
12.345
-0.6845
-2.0822
0.2342
2.4969
29.2565
-0.4272
-0.5096
-0.4616
0.6803
-0.2276
-0.0248
0.7291
-1.5462
0.6548
0.1685
-0.0721
0.0397
0.1134
0.0138
0.1488
32.3644
28.3072
53.6314
18
2.5606
-1.8603
1.5977
5.4704
-10.0504
20.183
0.58
0.5235
-0.1272
-0.5108
-0.1067
0.8628
0.3243
-1.1489
-0.4733
0.1399
0.0069
-0.1021
0.3646
-0.1408
0.2237
32.5988
33.019
28.577
19
2.6009
1.9561
-0.2386
20.1111
-3.5829
1.9617
0.0164
0.2004
-0.1478
-0.2679
-0.163
0.874
0.4443
-0.7183
0.1465
0.1837
0.0117
0.0325
0.3675
-0.0289
0.216
33.4072
35.9618
29.566
20
12.114
12.6195
-1.0799
19.3478
-5.0296
2.5546
-0.2286
-0.1226
-0.2348
-0.5086
-0.2943
-1.0031
0.0141
-0.2178
0.5229
0.293
0.0801
0.0116
0.3044
-0.0385
0.1792
43.4062
37.4104
29.7622
21
0.6825
-1.2795
5.6572
14.0734
2.5429
61.7048
-0.7323
0.3111
-0.3875
-3.0205
0.8971
-1.4891
1.1917
-0.5771
-0.1648
0.5232
-0.151
0.31
0.5774
0.0351
0.6496
46.5508
41.942
19.5206
22
13.7331
1.5749
11.0134
5.7052
2.6296
13.5498
0.0516
0.8368
-0.0681
-0.7371
-0.4692
-1.6195
0.9368
1.0433
0.4176
0.2427
0.0416
0.11
0.2919
-0.1044
0.213
42.9261
31.2021
24.267
23
7.7919
1.4234
-0.6581
6.1643
10.2494
24.3827
0.0313
0.053
-1.0509
0.4086
-0.2237
-0.2859
1.0988
0.4313
0.1924
0.1859
0.0782
0.0129
0.0593
0.0494
0.2425
39.9506
26.2203
46.6938
24
30.3356
24.0891
8.8621
32.084
7.8627
19.6218
0.0512
-1.2136
-1.4522
-0.4726
-0.1869
-1.6088
-0.1944
0.0473
0.1357
0.2862
0.0504
0.1392
0.2996
-0.005
0.199
37.7053
27.7785
41.5603
25
2.8227
-1.5632
3.7783
21.1544
15.9045
21.0215
0.0912
-0.2667
-0.2194
-0.6001
-0.2043
0.4765
0.1916
-0.3725
0.1131
0.0833
-0.0468
0.0524
0.3066
0.0486
0.1681
33.1566
28.0198
40.6813
26
6.7295
-9.577
-17.5995
30.3583
8.4705
62.4522
0.6649
-0.1044
0.7943
0.4116
-0.4307
0.5463
-0.5157
-1.9052
-0.2342
0.136
-0.086
0.081
0.3269
-0.0938
0.2168
34.1249
38.7199
54.5092
27
0.023
-0.7281
0.1162
23.0754
-3.0309
6.6711
-0.702
-1.3173
-0.1314
1.6302
0.0765
-1.2493
0.7312
1.1935
0.6255
0.1829
0.0256
-0.1244
0.5628
0.1103
0.117
49.9293
44.398
60.0326
28
3.5888
2.2992
-2.4947
3.4315
3.178
13.3823
0.3814
-0.7074
0.934
-1.2302
-0.2945
-0.4374
-0.7391
0.9134
-0.0868
0.3925
0.0436
0.1496
0.2553
0.0613
0.2961
49.0917
58.3234
38.5772
29
18.1097
-6.1116
9.8026
8.3471
-4.6278
13.2601
0.7927
0.554
0.4238
-0.0331
-0.6188
-0.3614
-0.2492
0.4995
-0.1739
0.2029
0.1214
0.0403
0.1918
0.0771
0.1366
48.0618
51.3666
31.0856
30
3.6626
2.1073
2.5817
3.598
3.4884
11.347
0.0851
-0.5392
0.8219
0.57
-0.3004
0.5365
-0.7118
-0.0603
0.2154
0.3919
0.0852
0.0484
0.09
-0.0096
0.3679
42.8097
56.8763
39.4311
31
34.4604
11.9174
18.74
21.8987
11.0488
11.3648
0.4587
-2.3081
1.0451
-1.9188
-1.6945
0.7499
-1.7407
-3.6993
1.2358
0.3748
0.4724
0.1142
0.5285
0.0578
0.1431
36.5677
61.1806
32.0296
32
4.8307
-1.9714
-1.64
18.9153
-5.518
20.0211
0.4819
-0.6121
0.813
2.177
-0.7089
0.6279
-1.1136
-0.2182
0.2271
0.0995
0.0345
0.0908
0.2321
-0.1142
0.0355
43.8338
51.844
56.7742
33
25.2884
21.5747
19.5374
18.6292
16.1303
16.3932
0.0391
-1.1464
0.7213
-1.8819
0.7908
0.3119
-0.3334
-0.9907
-0.83
0.2949
0.1385
0.1363
0.521
0.2673
0.6482
35.8549
48.7538
54.3948
34
6.5166
-4.8102
4.1504
10.8837
-4.3864
26.2743
1.0245
-0.1123
-0.3516
1.4924
0.0308
0.6314
-0.3246
-0.3109
-1.0553
0.176
0.0115
0.0906
0.2603
-0.0054
0.2151
45.3455
52.6825
50.2745
35
5.7019
9.2547
-0.6418
30.3953
-2.675
7.1409
0.476
-0.703
-0.1163
0.4225
-0.5664
-1.1645
-0.1954
0.3838
0.0905
0.1384
0.08
-0.0044
0.3812
-0.0594
0.2257
48.5523
46.2132
52.6499
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
X-RAY DIFFRACTION
1
A
A
5 - 14
5 - 14
2
X-RAY DIFFRACTION
2
A
A
15 - 29
15 - 29
3
X-RAY DIFFRACTION
3
A
A
30 - 45
30 - 45
4
X-RAY DIFFRACTION
4
A
A
46 - 65
46 - 65
5
X-RAY DIFFRACTION
5
A
A
66 - 80
66 - 80
6
X-RAY DIFFRACTION
6
A
A
81 - 93
81 - 93
7
X-RAY DIFFRACTION
7
A
A
94 - 100
94 - 100
8
X-RAY DIFFRACTION
8
A
A
101 - 113
101 - 113
9
X-RAY DIFFRACTION
9
A
A
114 - 137
114 - 137
10
X-RAY DIFFRACTION
10
B
B
4 - 30
4 - 30
11
X-RAY DIFFRACTION
11
B
B
31 - 64
31 - 64
12
X-RAY DIFFRACTION
12
B
B
65 - 79
65 - 79
13
X-RAY DIFFRACTION
13
B
B
80 - 96
80 - 96
14
X-RAY DIFFRACTION
14
B
B
97 - 108
97 - 108
15
X-RAY DIFFRACTION
15
B
B
109 - 116
109 - 116
16
X-RAY DIFFRACTION
16
B
B
117 - 137
117 - 137
17
X-RAY DIFFRACTION
17
C
C
4 - 14
4 - 14
18
X-RAY DIFFRACTION
18
C
C
15 - 28
15 - 28
19
X-RAY DIFFRACTION
19
C
C
29 - 50
29 - 50
20
X-RAY DIFFRACTION
20
C
C
51 - 64
51 - 64
21
X-RAY DIFFRACTION
21
C
C
65 - 72
65 - 72
22
X-RAY DIFFRACTION
22
C
C
73 - 81
73 - 81
23
X-RAY DIFFRACTION
23
C
C
82 - 100
82 - 100
24
X-RAY DIFFRACTION
24
C
C
101 - 117
101 - 117
25
X-RAY DIFFRACTION
25
C
C
118 - 128
118 - 128
26
X-RAY DIFFRACTION
26
C
C
129 - 137
129 - 137
27
X-RAY DIFFRACTION
27
D
D
4 - 14
4 - 14
28
X-RAY DIFFRACTION
28
D
D
15 - 28
15 - 28
29
X-RAY DIFFRACTION
29
D
D
29 - 38
29 - 38
30
X-RAY DIFFRACTION
30
D
D
39 - 65
39 - 65
31
X-RAY DIFFRACTION
31
D
D
66 - 81
66 - 81
32
X-RAY DIFFRACTION
32
D
D
82 - 96
82 - 96
33
X-RAY DIFFRACTION
33
D
D
97 - 101
97 - 101
34
X-RAY DIFFRACTION
34
D
D
109 - 116
109 - 116
35
X-RAY DIFFRACTION
35
D
D
117 - 137
117 - 137
+
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