MOLPROBITY STRUCTURE VALIDATION PROGRAMS : MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS : I.W. ...MOLPROBITY STRUCTURE VALIDATION PROGRAMS : MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS : I.W.DAVIS,J.M.WORD URL : HTTP://KINEMAGE.BIOCHEM.DUKE.EDU/MOLPROBITY/ AUTHORS : J.S.RICHARDSON,W.B.ARENDALL,D.C.RICHARDSON REFERENCE : NEW TOOLS AND DATA FOR IMPROVING : STRUCTURES, USING ALL-ATOM CONTACTS : METHODS IN ENZYMOLOGY. 2003;374:385-412. MOLPROBITY OUTPUT SCORES: ALL-ATOM CLASHSCORE : 15.09 (9.18 B<40) BAD ROTAMERS : 9.0% 25/277 (TARGET 0-1%) RAMACHANDRAN OUTLIERS : 4.4% 14/318 (TARGET 0.2%) RAMACHANDRAN FAVORED : 85.8% 273/318 (TARGET 98.0%)
Remark 999
SEQUENCE The sequence of myosin A tail domain interacting protein is not available at SWS and ...SEQUENCE The sequence of myosin A tail domain interacting protein is not available at SWS and Gebank databases at the time of processing.
Mass: 14812.686 Da / Num. of mol.: 3 / Fragment: myosin A tail domain interacting protein MTIP Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium knowlesi (eukaryote) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21STAR(DE3) / References: UniProt: D0VWV5*PLUS
#2: Protein/peptide
MyosinA / MyoA
Mass: 1843.290 Da / Num. of mol.: 1 / Fragment: myosin A / Source method: obtained synthetically Details: The sequence of this peptide naturally exists in Plasmodium yoelli References: UniProt: Q7RQ71*PLUS
Resolution: 2.6→2.739 Å / Redundancy: 9.6 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.799 / % possible all: 100
-
Processing
Software
Name
Version
Classification
REFMAC
5.2.0005
refinement
MOSFLM
datareduction
XDS
datascaling
SHELXS
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.868 / SU B: 29.053 / SU ML: 0.311 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.993 / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: RESIDUES 156 - 159, 183, 185, 188, 189 OF CHAIN B WERE MODELED WITHOUT SIDE CHAINS AS NO SIDE CHAIN DENSITY IS OBSERVABLE.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.28326
693
5 %
RANDOM
Rwork
0.22658
-
-
-
obs
0.22938
13219
99.93 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 44.113 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.46 Å2
0.73 Å2
0 Å2
2-
-
1.46 Å2
0 Å2
3-
-
-
-2.18 Å2
Refinement step
Cycle: LAST / Resolution: 2.6→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2949
0
0
71
3020
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.006
0.022
3002
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
0.939
1.954
4033
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.327
5
363
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.823
25.155
161
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.013
15
564
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
10.448
15
18
X-RAY DIFFRACTION
r_chiral_restr
0.072
0.2
438
X-RAY DIFFRACTION
r_gen_planes_refined
0.002
0.02
2271
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.174
0.2
1296
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.286
0.2
2099
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.105
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
0.182
0.2
78
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.131
0.2
11
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
1.045
4
1874
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.49
6
2905
X-RAY DIFFRACTION
r_scbond_it
1.592
6
1269
X-RAY DIFFRACTION
r_scangle_it
2.489
10
1127
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.6→2.739 Å / Total num. of bins used: 10
Rfactor
Num. reflection
% reflection
Rfree
0.383
106
-
Rwork
0.267
1897
-
obs
-
-
100 %
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
4.866
0.3879
0.2494
8.5217
-0.2601
8.7921
-0.2551
-0.0864
-0.1055
0.0866
0.4744
0.1069
-0.2765
0.3807
-0.2194
-0.0496
-0.0024
-0.018
-0.0192
0.0337
-0.1152
61.2316
-3.062
17.7353
2
18.3013
-1.7981
1.8845
2.4051
-0.6241
0.2805
-0.0269
0.3079
0.0028
-0.3392
-0.0502
0.0637
0.1011
0.4973
0.0771
-0.0085
-0.0343
0.0178
0.0504
0.0824
-0.0929
61.2788
-3.0603
9.0198
3
39.2023
3.5811
-1.6786
4.377
-4.0608
7.7179
0.2545
-0.0754
0.17
-0.192
-0.0777
-0.1139
-0.3945
-0.3442
-0.1768
0.0689
0.0381
0.0449
-0.1536
0.1057
-0.0189
37.6746
-7.1178
7.104
4
27.7073
-17.0592
3.1707
25.5772
-4.0768
7.0812
0.7755
0.1989
0.941
0.1167
-0.6065
0.7565
-0.5813
-0.0124
-0.169
-0.085
-0.1067
0.1453
0.0107
0.0884
0.039
29.703
-11.4586
14.8907
5
5.9148
3.3365
-3.5451
8.1534
-6.5246
9.7341
-0.2189
-0.2197
-0.501
-0.1027
0.0974
-0.44
-0.2426
-0.3036
0.1215
-0.0563
-0.0235
-0.03
-0.0683
-0.052
0.0451
40.115
-16.1587
6.6916
6
10.2388
-1.5615
-13.372
0.3163
0.783
37.6718
0.8071
-1.394
-1.2567
-0.0602
-0.518
-1.0653
1.0049
1.0838
-0.2891
-0.0976
-0.184
-0.1139
0.0212
0.2258
0.1121
45.3246
-19.6611
14.7196
7
5.8116
-3.0657
2.3361
13.2774
-4.8325
13.8062
0.0981
-0.4687
0.6451
2.1771
-0.5887
-0.9343
-1.7335
0.1262
0.4906
0.1321
-0.2522
-0.0856
-0.0347
0.0749
-0.0388
38.5
-10.8272
18.8777
8
0.4604
-1.9753
-0.8649
10.2724
0.3456
7.928
-0.3137
0.6807
0.4969
-0.4507
0.036
-0.8683
-0.1013
0.368
0.2777
-0.1199
0.0288
0.0306
0.0472
-0.0251
0.0711
40.7644
10.9387
-17.8207
9
9.4505
-9.6648
2.7531
11.9529
-8.9262
18.8495
0.0446
-0.2705
-1.9854
-0.2834
-0.0555
0.0766
0.1626
0.5744
0.0109
-0.0327
0.179
0.1004
-0.2722
-0.1217
0.0257
40.4058
1.7849
-13.8641
10
3.1146
5.163
2.5657
16.1336
0.508
3.9652
-0.0022
0.3173
0.1011
-0.5204
0.2354
0.596
0.0182
-0.1566
-0.2332
-0.0099
0.0325
-0.0001
-0.0594
0.001
-0.0232
31.0179
10.9492
-14.7303
11
2.8705
-5.4173
0.2864
10.5398
-1.5586
3.3072
-0.2895
0.0868
-0.0836
0.5626
0.1584
-0.2305
0.1834
-0.2236
0.131
0.0655
0.0462
-0.0267
-0.0488
0.0011
-0.0331
38.0503
9.3288
-7.2158
12
4.2347
0.694
5.3077
45.3423
-6.7037
7.9208
0.3216
0.1827
0.0085
-0.3715
-0.1581
0.1059
0.6771
0.2616
-0.1636
0.079
-0.0522
0.0055
-0.0711
-0.019
-0.1183
38.277
-11.1211
-5.0633
13
19.9655
0.1969
-5.049
32.1686
-18.6773
12.0639
-0.2281
1.6461
-2.7232
-2.0705
-0.9927
-0.9924
2.3375
1.7646
1.2208
0.4333
0.165
0.2512
-0.1595
-0.2904
0.0493
34.7121
-24.4552
-8.9011
14
2.3244
-4.974
5.6721
20.2494
6.6957
50.7722
0.5414
-0.3693
-1.4924
-0.5037
-0.1389
0.4405
-0.7351
-0.717
-0.4025
-0.328
-0.2951
-0.0233
0.0348
0.2165
0.075
26.4586
-18.2146
-4.1531
15
16.7218
6.6043
2.9283
2.8224
4.1606
42.6727
-0.8779
0.0587
-0.7619
0.1194
0.5145
1.0192
-1.0395
0.0124
0.3634
0.0565
-0.0474
-0.1393
-0.044
0.1069
0.071
23.1823
-11.5565
-10.6157
16
15.1431
-16.346
2.8253
56.8082
-21.2229
8.9601
0.6064
0.4373
0.0387
-1.2769
0.371
-0.4245
0.6664
0.5876
-0.9774
0.4024
-0.0414
-0.0725
-0.0692
-0.273
-0.1665
36.023
-12.7456
-14.1301
17
45.2427
-8.6815
1.7367
37.5289
-8.4118
1.8865
-0.0332
-2.0075
0.1503
0.0125
-0.6031
0.0746
-1.3045
-0.9917
0.6362
-0.0314
0.0409
0.0647
0.0308
0.0904
-0.2573
30.5899
-2.4771
1.4629
18
1.8151
-3.2485
2.4736
10.4285
1.7583
11.6615
-0.1327
-0.3791
-1.0863
0.3493
0.1615
0.6287
0.1035
-0.5511
-0.0288
-0.1181
-0.0503
0.0057
-0.0203
0.1882
0.0441
45.4462
7.1162
5.421
19
19.2387
1.2974
4.8332
13.2011
0.7708
5.7336
0.4975
-0.9066
0.7019
1.5814
0.1181
0.2954
0.0088
-0.2047
-0.6156
0.0343
0.0279
0.0623
-0.0241
-0.0578
-0.1264
43.3321
16.1351
11.3639
20
22.1867
-3.2149
-11.0934
3.1911
7.7996
19.6161
-0.0914
-0.8268
0.4895
0.3979
0.1678
-0.1825
-1.0047
0.1403
-0.0764
0.0589
0.0268
-0.0111
-0.1359
0.0451
-0.002
43.7405
16.0697
2.9018
21
43.2445
-7.4465
-14.2559
6.297
-0.0581
12.4785
-0.0294
-0.1849
-0.8014
-0.2898
-0.0401
-0.0312
0.4369
-0.0749
0.0694
0.0737
-0.0522
-0.0308
-0.2362
-0.0017
-0.0781
59.9852
13.1103
-6.2339
22
4.8646
-2.3754
0.3004
12.2607
-0.1001
10.5113
-0.2724
0.128
-0.8048
-0.6613
0.2358
-0.8001
0.6997
0.4524
0.0366
-0.0627
0.0781
0.0589
-0.1453
0.0549
0.0414
75.6242
9.3309
-7.6653
23
8.5106
-0.2674
2.5562
6.0084
-0.6823
3.9956
-0.1262
-0.3634
-0.674
-0.0927
-0.0611
-0.3479
0.4098
0.1316
0.1873
-0.0084
0.0322
0.0563
-0.0695
0.1283
-0.0288
73.6719
8.1189
1.9166
24
10.186
-2.6563
0.0747
6.1565
4.1444
17.8753
-0.8256
-0.4699
-0.0235
0.7808
-0.2385
0.1358
-0.2595
-0.271
1.064
-0.0185
-0.0682
-0.0658
-0.1155
0.093
0.0234
69.0687
17.584
4.1878
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
88 - 117
10 - 39
2
X-RAY DIFFRACTION
2
A
A
118 - 140
40 - 62
3
X-RAY DIFFRACTION
3
A
A
141 - 152
63 - 74
4
X-RAY DIFFRACTION
4
A
A
153 - 162
75 - 84
5
X-RAY DIFFRACTION
5
A
A
163 - 176
85 - 98
6
X-RAY DIFFRACTION
6
A
A
177 - 188
99 - 110
7
X-RAY DIFFRACTION
7
A
A
189 - 203
111 - 125
8
X-RAY DIFFRACTION
8
B
B
89 - 101
11 - 23
9
X-RAY DIFFRACTION
9
B
B
102 - 110
24 - 32
10
X-RAY DIFFRACTION
10
B
B
111 - 124
33 - 46
11
X-RAY DIFFRACTION
11
B
B
125 - 137
47 - 59
12
X-RAY DIFFRACTION
12
B
B
138 - 151
60 - 73
13
X-RAY DIFFRACTION
13
B
B
152 - 162
74 - 84
14
X-RAY DIFFRACTION
14
B
B
163 - 173
85 - 95
15
X-RAY DIFFRACTION
15
B
B
174 - 189
96 - 111
16
X-RAY DIFFRACTION
16
B
B
195 - 204
117 - 126
17
X-RAY DIFFRACTION
17
C
C
79 - 85
1 - 7
18
X-RAY DIFFRACTION
18
C
C
89 - 109
11 - 31
19
X-RAY DIFFRACTION
19
C
C
115 - 125
37 - 47
20
X-RAY DIFFRACTION
20
C
C
126 - 135
48 - 57
21
X-RAY DIFFRACTION
21
C
C
136 - 149
58 - 71
22
X-RAY DIFFRACTION
22
C
C
150 - 173
72 - 95
23
X-RAY DIFFRACTION
23
C
C
174 - 204
96 - 126
24
X-RAY DIFFRACTION
24
D
D
803 - 816
1 - 14
+
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