Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Compound details
ENGINEERED RESIDUE IN CHAIN A, LYS 294 TO ALA ENGINEERED RESIDUE IN CHAIN A, CYS 411 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, LYS 294 TO ALA ENGINEERED RESIDUE IN CHAIN A, CYS 411 TO ALA ENGINEERED RESIDUE IN CHAIN A, ALA 423 TO CYS ENGINEERED RESIDUE IN CHAIN B, LYS 294 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS 411 TO ALA ENGINEERED RESIDUE IN CHAIN B, ALA 423 TO CYS
Sequence details
K294A IS AN ENGINEERED MUTATION. C411A AND A423C HAVE ALSO BEEN INTRODUCED TO GIVE HIGHER ...K294A IS AN ENGINEERED MUTATION. C411A AND A423C HAVE ALSO BEEN INTRODUCED TO GIVE HIGHER EXPRESSION. THE PROTEIN WITH THESE TWO MUTATIONS BEHAVES LIKE WILD-TYPE. UNK RESIDUES B 12-27 REPRESENT SECTION OF CHAIN B STRUCTURE WITH NO ASSIGNED SEQUENCE. ACTUAL SEQUENCE OF CHAIN B IS SUPPOSED TO BE IDENTICAL TO CHAIN A, FOR RESIDUES 1-50, SEQUENCE ASSIGNMENT COULD NOT BE DONE IN THE ELECTRON DENSITY DUE TO UNKNOWN REGISTER.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 4
-
Sample preparation
Crystal
Density Matthews: 4.3 Å3/Da / Density % sol: 71.4 % Description: 5 DATASETS WERE COLLECTED ON 4 CRYSTALS AND MERGED
Resolution: 2.73→68.01 Å / Cor.coef. Fo:Fc: 0.8345 / Cor.coef. Fo:Fc free: 0.8639 / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE ELECTRON DENSITY QUALITY WAS BETTER FOR CHAIN A. CHAIN B WAS BUILT LARGELY WITH CHAIN A AS A MODEL.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2743
2690
5.07 %
RANDOM
Rwork
0.2509
-
-
-
obs
0.252
53054
-
-
Displacement parameters
Biso mean: 112.01 Å2
Baniso -1
Baniso -2
Baniso -3
1-
5.914 Å2
0 Å2
0 Å2
2-
-
-10.0441 Å2
0 Å2
3-
-
-
4.1301 Å2
Refine analyze
Luzzati coordinate error obs: 0.604 Å
Refinement step
Cycle: LAST / Resolution: 2.73→68.01 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
8064
0
21
5
8090
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
8219
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.16
11197
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
2594
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
106
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
1201
HARMONIC
5
X-RAY DIFFRACTION
t_it
8201
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
2.38
X-RAY DIFFRACTION
t_other_torsion
21.68
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
1143
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_sum_occupancies
X-RAY DIFFRACTION
t_utility_distance
X-RAY DIFFRACTION
t_utility_angle
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
10446
SEMIHARMONIC
4
LS refinement shell
Resolution: 2.73→2.8 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.3008
41
5.83 %
Rwork
0.231
662
-
all
0.2347
703
-
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
1.1265
-0.153
-0.7847
2.0942
0.6775
6.1163
-0.0244
0.3191
0.2487
-0.5442
-0.1337
-0.1469
-0.3091
-0.2233
0.1581
0.3033
0.0572
-0.034
-0.304
0.0657
0.0575
-1.6965
-36.4554
-61.944
2
0.4268
0.7132
-1.7602
0.6474
1.1637
0.9932
0.0039
-0.0394
-0.0111
0.0062
-0.0477
0.0589
-0.0105
0.0356
0.0438
-0.1194
0.152
-0.008
-0.2563
-0.0739
0.2285
-7.8592
-24.2407
-40.729
3
0
-0.713
-1.1859
3.5612
-1.011
0.0747
0.0106
-0.1515
0.052
-0.0142
0.0307
0.0229
-0.0739
0.0014
-0.0412
0.304
-0.066
-0.152
-0.3004
0.1155
0.2242
1.6953
-18.2678
-42.4709
4
1.3292
0.0761
0.072
5.0349
0.4435
3.5498
-0.0336
0.2097
0.0395
-0.5442
-0.0605
-0.0401
0.5442
0.218
0.0941
0.304
0.1141
-0.0285
-0.3036
0.0419
0.0733
1.8908
-41.9267
-56.6007
5
1.3677
0.6315
-0.8207
5.9188
-0.7666
3.2232
-0.0977
-0.072
0.1232
-0.405
-0.3172
-0.5442
-0.113
0.5442
0.415
-0.2998
0.152
-0.0684
-0.304
0.0808
0.0685
11.5872
-35.2304
-48.4237
6
0.2764
0.6125
-0.8286
0.424
-1.1426
0
0.0064
0.0279
0.0156
0.0491
-0.0125
-0.0016
0.0112
0.038
0.0061
-0.3034
0.0989
-0.034
0.1296
0.0916
0.0201
5.7787
-37.5328
-29.6229
7
1.2195
-2.839
-0.6863
8.3155
2.9104
3.2589
0.0396
-0.3889
0.3533
0.048
-0.086
0.2286
-0.2085
0.2537
0.0464
0.304
0.0264
-0.152
-0.2568
-0.1029
0.0503
2.7066
-22.254
-24.9116
8
2.0138
0.2351
1.2717
4.8842
-1.2737
3.5105
0.0565
-0.0009
-0.1965
-0.164
0.0679
0.5442
0.2571
-0.5311
-0.1244
-0.0509
-0.0119
-0.0714
-0.304
-0.1
0.2925
-17.632
-41.4935
-49.4698
9
1.1365
-1.2445
2.4379
0.368
-1.2582
0.5353
0.0228
0.0726
-0.0401
-0.0625
0.0384
0.0317
0.0292
-0.0053
-0.0612
0.1221
0.085
-0.1503
-0.1692
0.0881
0.0706
-12.8125
-27.3577
-68.5656
10
0.0513
0.2664
1.826
8.3155
-2.8475
6.7128
0.0793
-0.5442
-0.3059
-0.0958
-0.0676
0.3178
0.0236
-0.0011
-0.0117
0.304
0.152
-0.0207
-0.2001
0.152
-0.304
1.8061
-53.8813
-0.1481
11
0.0492
1.2872
0.2316
0.1044
0.7108
0.3041
0.0045
-0.0587
-0.0046
0.0511
0.0097
0.0487
0.0174
0.046
-0.0143
0.2898
-0.0294
-0.1177
-0.1373
-0.1416
-0.1674
1.8837
-31.4724
-10.1802
12
0
1.172
-2.9104
0.1462
1.8088
0.5574
-0.0052
-0.0593
0.0332
0.0346
0.0146
-0.0277
-0.0581
-0.0206
-0.0093
0.2922
0.113
0.15
-0.1536
-0.152
-0.0545
-8.8451
-30.4959
-6.4321
13
0.0671
0.804
0.3247
2.9025
-2.365
4.8545
0.1271
-0.5442
-0.4551
0.5442
-0.4043
0.3352
0.5442
0.342
0.2772
0.304
0.152
0.152
-0.304
0.152
-0.304
-0.3645
-56.735
-7.1714
14
1.5256
-0.3869
-1.3541
2.187
0.1714
3.4124
-0.0032
-0.5442
-0.1708
0.5242
-0.1468
0.2911
0.4684
-0.5431
0.15
0.304
-0.0314
0.152
-0.304
0.0221
-0.304
-12.9392
-49.6288
-12.0126
15
0
0.1723
0.5136
0
0.7897
0
0.0073
-0.0135
-0.0046
0.0182
-0.0063
0.046
-0.0058
-0.0415
-0.001
0.1242
0.113
0.0886
-0.2752
-0.0547
-0.1888
-7.993
-40.4691
-27.6962
16
0
0.8672
-1.2249
4.8105
2.149
1.6895
-0.0568
-0.0438
0.1784
0.1702
0.0375
0.0118
-0.0117
-0.1351
0.0193
0.304
0.152
0.152
-0.304
-0.152
-0.0908
-10.1277
-24.8782
-23.5162
17
2.458
-2.9104
2.9104
3.3803
0.886
7.4479
0.0301
-0.3452
-0.2257
0.0219
-0.0544
-0.3117
-0.1961
0.4616
0.0243
0.2813
0.1309
-0.152
-0.2995
0.1519
-0.2706
17.1809
-46.2544
-10.9783
18
0
-1.7027
0.6174
0.0043
-1.0035
0.6175
0.0097
-0.0035
0.0251
-0.006
-0.0156
0.0549
0.0331
0.0224
0.0059
0.1471
0.0787
-0.1006
0.0339
0.0965
-0.2167
9.7824
-47.7387
12.2016
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
(A10 - A97 )
2
X-RAY DIFFRACTION
2
(A98 - A107 )
3
X-RAY DIFFRACTION
3
(A108 - A117 )
4
X-RAY DIFFRACTION
4
(A118 - A338 )
5
X-RAY DIFFRACTION
5
(A339 - A486 )
6
X-RAY DIFFRACTION
6
(A487 - A491 )
7
X-RAY DIFFRACTION
7
(A492 - A516 )
8
X-RAY DIFFRACTION
8
(A517 - A561 )
9
X-RAY DIFFRACTION
9
(A562 - A573 )
10
X-RAY DIFFRACTION
10
(B12 - B97 )
11
X-RAY DIFFRACTION
11
(B98 - B107 )
12
X-RAY DIFFRACTION
12
(B108 - B117 )
13
X-RAY DIFFRACTION
13
(B118 - B338 )
14
X-RAY DIFFRACTION
14
(B339 - B486 )
15
X-RAY DIFFRACTION
15
(B487 - B491 )
16
X-RAY DIFFRACTION
16
(B492 - B516 )
17
X-RAY DIFFRACTION
17
(B517 - B561 )
18
X-RAY DIFFRACTION
18
(B562 - B573 )
+
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