A: Transcriptional regulator, RpiR family B: Transcriptional regulator, RpiR family C: Transcriptional regulator, RpiR family D: Transcriptional regulator, RpiR family
Resolution: 1.8→1.83 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.655 / Mean I/σ(I) obs: 2 / Num. unique all: 3358 / % possible all: 99.3
-
Processing
Software
Name
Version
Classification
SBC-Collect
datacollection
SHELX
modelbuilding
MLPHARE
phasing
DM
modelbuilding
ARP/wARP
modelbuilding
Coot
modelbuilding
BUSTER
2.8.0
refinement
HKL-3000
datareduction
HKL-3000
datascaling
SHELX
phasing
DM
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.8→35.45 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.9387 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML Details: The crystals were obtain by in situ proteolysis with chymotrypsin, which apparently cut the N-terminal DNA-binding domain (residues ~ 1-90) prior to crystal formation. The precise location ...Details: The crystals were obtain by in situ proteolysis with chymotrypsin, which apparently cut the N-terminal DNA-binding domain (residues ~ 1-90) prior to crystal formation. The precise location of the cleavage site has not been determined. The region near residues 191-193 contains unknown density that has not been modeled.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2092
1198
1.75 %
thin resolution shells
Rwork
0.1729
-
-
-
all
0.1735
68604
-
-
obs
0.1735
68604
99.8 %
-
Displacement parameters
Biso mean: 34.96 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-8.0909 Å2
0 Å2
-0.7281 Å2
2-
-
0.3685 Å2
0 Å2
3-
-
-
7.7224 Å2
Refine analyze
Luzzati coordinate error obs: 0.216 Å
Refinement step
Cycle: LAST / Resolution: 1.8→35.45 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5443
0
0
304
5747
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.015
5557
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.17
7609
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
2571
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
129
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
828
HARMONIC
5
X-RAY DIFFRACTION
t_it
5537
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
3.47
X-RAY DIFFRACTION
t_other_torsion
2.6
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
774
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
6822
SEMIHARMONIC
4
LS refinement shell
Resolution: 1.8→1.85 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.2138
64
1.27 %
Rwork
0.2183
4957
-
all
0.2182
5021
-
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
8.4755
-1.7109
-0.7721
2.3448
-0.0658
3.1038
-0.036
0.1406
-0.1985
-0.0519
-0.0607
-0.0605
0.1417
0.134
0.0967
0.1622
0.0353
0.0288
-0.1025
-0.0047
-0.1393
54.5683
15.4882
-19.2329
2
1.6877
0.1792
0.1176
1.5696
-0.1358
1.1331
0.0387
0.0702
0.0115
0.0343
-0.0217
0.0358
-0.1068
-0.1451
-0.017
0.0403
0.0266
0.0056
-0.0754
-0.006
-0.0731
38.3274
23.7179
-1.2132
3
1.5138
0.6195
-2.26
0.0824
1.0791
7.7496
0.0049
-0.2869
0.1745
0.5327
-0.1182
0.0584
0.417
0.0171
0.1133
0.1983
-0.0473
-0.0273
-0.07
-0.0413
-0.0945
34.9707
16.7804
11.2441
4
1.4421
0.6884
-0.379
2.0071
-0.554
2.1553
0.0369
0.0836
-0.0959
-0.0144
-0.0647
-0.051
0.2666
-0.1279
0.0278
0.0604
-0.0277
-0.0059
-0.09
-0.0201
-0.0542
37.4044
10.6501
-2.6752
5
0.9801
0.0253
-0.6085
0.8193
0.8028
1.4588
-0.0651
0.1217
-0.0815
0.1017
-0.1315
0.0934
0.0365
-0.1166
0.1967
0.0796
0.0292
0.0009
-0.0679
0.0137
-0.0844
43.2695
27.1866
-6.7123
6
0.8886
-1.3496
0.3178
0.9725
1.8905
0.758
0.015
0.1883
0.1041
0.0373
-0.0421
-0.017
-0.0448
0.0847
0.0271
0.2588
-0.0337
-0.0265
-0.1681
0.0732
-0.0665
48.1234
45.6637
9.1655
7
3.1157
-1.5727
1.165
0.009
-0.7862
0.2349
-0.0032
0.2278
0.1003
-0.2424
0.049
0.0991
-0.0781
-0.2275
-0.0458
0.15
0.0733
-0.0182
-0.0024
0.0271
-0.0861
42.6284
28.3422
-19.0655
8
2.7065
-0.331
0.0926
1.318
-0.0981
1.9068
0.0544
0.1309
0.0503
-0.1421
-0.0005
-0.0266
0.0494
0.0338
-0.0539
0.0745
0.0016
0.0371
-0.1607
0.0069
-0.0729
63.9474
22.3917
-6.8423
9
0.1887
1.6333
0.8975
4.6437
1.4367
3.6613
0.1247
-0.0687
-0.157
0.4275
-0.0661
0.2141
-0.2027
-0.1286
-0.0587
0.1628
0.0175
0.067
-0.0459
0.026
-0.0633
62.5468
20.576
7.8469
10
1.6553
-0.0636
0.7858
2.3346
0.3421
2.9092
-0.0491
-0.0335
0.0113
0.1942
0.0432
-0.0293
-0.3391
0.2107
0.0059
0.0938
-0.0426
0.0299
-0.115
0.0142
-0.0531
67.0733
30.8013
0.2615
11
1.2614
-0.8008
0.1816
3.3029
-0.2185
1.3422
0.0167
0.081
0.2028
-0.1115
-0.1371
-0.0327
-0.1072
0.032
0.1203
0.0775
0.0067
0.0062
-0.0931
-0.0001
-0.0762
56.9144
23.8481
-10.2514
12
3.4861
0.6933
-2.6478
1.8228
1.6295
1.2353
0.0124
0.1894
-0.0652
0.2095
-0.2183
0.0492
0.1093
0.0222
0.2058
0.1656
0.0539
0.041
-0.1271
-0.0034
-0.0352
62.6263
1.2495
-0.1948
13
3.5109
-1.2474
2.1386
1.5567
-0.3909
0.7566
-0.0187
0.0135
0.0863
-0.0654
-0.1435
0.1191
0.055
-0.1228
0.1621
0.1128
-0.0163
0.0332
0.0227
-0.0151
-0.1441
36.8643
22.0008
42.3061
14
0.9991
-0.8943
-0.4308
0.8795
0.6851
3.2633
-0.0698
-0.1713
-0.0726
0.029
0.0233
0.0567
0.0975
0.1139
0.0465
0.1639
-0.0013
0.0153
-0.1174
0.0313
-0.1249
59.4058
11.7368
31.212
15
0.4954
0.6233
0.1618
0.3205
0.0336
3.7785
0.0274
-0.0081
0.0242
-0.1249
0.0229
0.0727
-0.1525
-0.1315
-0.0502
0.1701
0.0189
-0.004
-0.0925
0.0359
-0.1113
61.5204
12.341
15.8728
16
3.0084
-0.0494
-1.563
2.7103
1.4587
4.5047
-0.1158
0.1892
-0.3049
0.1964
-0.1433
0.3289
0.368
-0.3095
0.2591
0.2126
-0.0072
0.0446
-0.1555
0.0229
-0.1018
54.0963
2.2653
23.5302
17
1.6278
-1.3601
-0.8099
0.9003
0.3962
2.2229
-0.07
-0.1119
-0.2449
0.046
-0.0973
0.1889
0.023
-0.0193
0.1673
0.1612
0.0153
0.0383
-0.1175
0.0149
-0.1534
55.1255
13.4174
33.0639
18
2.0406
2.2102
-1.211
0.0226
-1.4822
0.7682
0.0432
-0.0772
0.2597
0.0311
0.1322
-0.1589
-0.1775
0.1372
-0.1754
0.2909
-0.1539
0.0329
-0.1334
0.0161
-0.1902
70.7817
30.5442
22.3119
19
2.2855
-2.8608
1.2363
1.2376
0.028
2.3569
0.0022
-0.0228
-0.0826
0.1012
0.0232
-0.0875
0.0823
0.1261
-0.0254
0.1676
0.0007
0.005
-0.0082
0.0303
-0.1165
62.9282
18.6367
42.2267
20
2.9911
-1.1324
0.2219
1.4587
-0.3965
2.1187
-0.1078
-0.2989
0.0309
0.2302
0.1239
0.071
0.0388
-0.2139
-0.0161
0.1476
0.0002
0.0214
-0.117
-0.0125
-0.153
42.1971
29.5135
30.6476
21
0.6217
0.5006
-0.5996
0.923
-0.5021
3.1045
-0.018
0.0531
-0.0275
-0.1027
-0.0218
0.0244
0.2746
-0.2087
0.0398
0.1282
0.0117
0.0206
-0.0575
-0.0263
-0.1134
40.8799
29.3557
16.251
22
3.8433
-0.707
0.5697
1.446
-0.3153
2.9459
0.0528
0.022
0.1771
0.0788
-0.0603
-0.0678
-0.3286
0.1032
0.0075
0.1849
-0.0052
0.0021
-0.1054
-0.0263
-0.1085
47.8158
39.2441
24.5562
23
3.8073
-0.8124
0.3716
0.993
0.0146
1.2992
-0.0564
-0.2734
0.1676
0.0569
-0.0261
-0.1146
0.0507
-0.1187
0.0826
0.1665
0.0127
0.0174
-0.076
0.0113
-0.1743
47.5327
26.812
33.5803
24
2.1327
-0.7632
2.769
0.0861
0.1244
1.157
-0.0273
-0.1612
-0.0906
0.0186
0.0814
0.0449
0.1188
-0.1263
-0.0541
0.2169
-0.1587
0.1137
-0.1545
0.0726
-0.0409
30.3541
12.8716
23.7535
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
chainA
2
X-RAY DIFFRACTION
2
chainB
3
X-RAY DIFFRACTION
3
chainC
4
X-RAY DIFFRACTION
4
chainD
+
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