HIT-like / HINT family / Histidine triad (HIT) protein / HIT domain / Histidine triad, conserved site / HIT domain signature. / HIT domain profile. / HIT-like domain / HIT-like / HIT family, subunit A ...HIT-like / HINT family / Histidine triad (HIT) protein / HIT domain / Histidine triad, conserved site / HIT domain signature. / HIT domain profile. / HIT-like domain / HIT-like / HIT family, subunit A / HIT-like superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal grow
Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30% PEG 8000, 0.2M NH4 Sulfate, 0.1M Na Cacodylate pH 6.5. Paratone-N was used for cryoprotection, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97857 Å / Relative weight: 1
Reflection
Resolution: 2→30 Å / Num. all: 77248 / Num. obs: 77248 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 33.6 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 14.92
Reflection shell
Resolution: 2→2.03 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 2.67 / Num. unique all: 3868 / % possible all: 100
-
Processing
Software
Name
Version
Classification
Blu-Ice
Max
datacollection
CRANK
phasing
SHELXCD
phasing
SHELXE
modelbuilding
bp3
modelbuilding
SOLOMON
phasing
ARP/wARP
modelbuilding
BUCCANEER
modelbuilding
REFMAC
5.5.0102
refinement
HKL-2000
datareduction
HKL-2000
datascaling
bp3
phasing
BUCCANEER
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.01→30 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 6.969 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. The Friedel pairs were used in phasing. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.19754
1998
5 %
RANDOM
Rwork
0.16091
-
-
-
all
0.16279
37836
-
-
obs
0.16279
37836
99.28 %
-
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: 20.402 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.45 Å2
0 Å2
-0.17 Å2
2-
-
-0.39 Å2
-0 Å2
3-
-
-
-1.12 Å2
Refinement step
Cycle: LAST / Resolution: 2.01→30 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4482
0
29
285
4796
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.011
0.022
4798
X-RAY DIFFRACTION
r_bond_other_d
0
0.02
3081
X-RAY DIFFRACTION
r_angle_refined_deg
1.472
1.928
6546
X-RAY DIFFRACTION
r_angle_other_deg
0.845
3
7618
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
3.877
5
606
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.28
25.801
231
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
10.323
15
802
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
10.177
15
5
X-RAY DIFFRACTION
r_chiral_restr
0.096
0.2
728
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
5459
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
922
X-RAY DIFFRACTION
r_mcbond_it
0.868
1.5
2958
X-RAY DIFFRACTION
r_mcbond_other
0.277
1.5
1188
X-RAY DIFFRACTION
r_mcangle_it
1.563
2
4828
X-RAY DIFFRACTION
r_scbond_it
2.616
3
1840
X-RAY DIFFRACTION
r_scangle_it
4.014
4.5
1718
LS refinement shell
Resolution: 2.01→2.06 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.226
137
-
Rwork
0.193
2563
-
obs
-
2563
92.91 %
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
3.3907
-0.1931
0.6196
1.6218
0.0769
2.0684
0.0985
-0.3437
-0.2432
0.2047
0.0229
-0.1261
0.052
-0.0577
-0.1214
0.0594
-0.0033
0.0037
0.0495
0.0503
0.0916
11.3324
-6.5499
47.2025
2
3.2084
0.4679
0.5991
0.9093
-0.1526
1.348
0.0277
0.049
-0.2359
0.0612
0.0173
-0.1677
0.0975
0.2092
-0.045
0.0512
0.0276
-0.0096
0.0467
0.0174
0.1297
19.2773
-2.9686
38.4622
3
2.4487
0.7483
0.6707
1.123
0.0698
1.8793
-0.0073
0.0311
0.0359
0.0346
0.0624
0.1255
-0.0986
-0.1449
-0.055
0.0153
0.0167
0.0131
0.0229
0.0234
0.0558
7.6832
2.8674
38.8242
4
6.3416
1.6551
-0.2833
3.1794
0.0509
0.9021
-0.1313
0.1617
0.8235
-0.0525
0.1781
0.1452
-0.2282
0.0396
-0.0468
0.1593
-0.0017
-0.0158
0.0628
0.0351
0.1155
18.1078
20.1561
32.2061
5
2.6826
0.4775
0.1072
2.3099
0.4916
2.9935
-0.1538
0.5135
0.112
-0.4572
0.1746
-0.076
-0.2378
0.134
-0.0208
0.1613
-0.047
0.0175
0.1181
0.046
0.0681
20.6414
13.2402
22.3021
6
3.277
0.864
0.9539
1.627
0.1867
2.382
-0.0151
0.314
-0.1838
-0.1973
0.0748
-0.1447
-0.0033
0.0826
-0.0596
0.0321
-0.0001
0.0189
0.0308
-0.0145
0.0291
20.1746
2.9606
28.2951
7
2.9066
0.6744
0.4105
1.9048
0.1178
2.3846
-0.0044
-0.0163
0.2477
-0.0196
-0.0079
0.1518
-0.2243
-0.1054
0.0123
0.0808
0.0214
0.0057
0.0172
0.0228
0.0759
13.2963
13.588
34.4155
8
4.6407
0.1427
-2.3076
1.5002
1.1166
4.7913
0.03
0.0366
-0.1439
0.0308
-0.1193
0.146
0.1357
-0.416
0.0892
0.0737
0.0014
-0.0416
0.1301
0.0519
0.0965
-1.1268
-6.2353
42.5692
9
5.3434
0.4456
0.7964
6.2816
-1.1489
3.7962
0.039
-0.7752
-0.3458
0.7105
-0.1822
0.2891
-0.2613
-0.275
0.1432
0.4046
-0.0096
0.0348
0.399
0.1198
0.1074
0.2013
-19.2612
95.4525
10
3.2849
0.6438
0.2268
3.1791
-0.5739
3.6765
0.0173
-0.3449
-0.0525
0.4779
-0.1557
0.0315
-0.1296
0.0744
0.1383
0.1927
-0.0286
-0.0012
0.2381
0.1254
0.078
3.7371
-16.3488
84.4522
11
11.6011
13.5286
7.7036
16.9606
10.2628
6.5802
0.0487
0.1119
-1.3223
0.5768
0.6329
-1.3069
0.6222
0.9032
-0.6816
0.5136
0.1571
-0.0872
1.0325
0.2683
0.635
18.5264
-21.6395
78.7253
12
6.3374
-1.5057
-0.5097
2.6198
0.2751
7.7011
-0.0682
0.3921
-0.3061
-0.2055
-0.0222
-0.0115
0.2416
-0.3263
0.0904
0.1496
-0.0968
0.0037
0.1149
0.0588
0.2266
-1.8493
-18.4284
58.6865
13
1.7599
0.6606
-0.34
2.4211
-0.4802
3.0474
0.0006
-0.0475
0.0934
0.1684
-0.0085
0.0536
-0.3082
0.0035
0.0079
0.1177
-0.0214
-0.0191
0.105
0.0571
0.1036
1.9428
-7.074
68.2614
14
3.7899
2.0968
-0.0203
3.8712
-0.7121
3.8794
-0.0578
-0.1873
-0.3245
-0.0505
-0.0693
-0.1828
0.2391
0.1481
0.1271
0.0921
0.0011
-0.0008
0.1045
0.0972
0.0976
4.9917
-17.946
70.5281
15
6.9355
0.5143
9.5121
0.7776
0.4064
24.5562
0.2258
-0.3729
-0.5251
0.2794
-0.2535
-0.2645
0.8668
0.8116
0.0277
0.3485
0.0245
-0.0158
0.3784
0.2879
0.4338
13.4358
-27.0559
84.968
16
18.6524
-10.7207
2.7866
32.6116
-11.5825
8.6256
-0.3181
-1.0194
0.6025
1.1233
0.0339
-0.5807
-0.7843
0.7734
0.2842
0.4624
-0.1915
-0.2133
0.5751
0.0743
0.1139
14.16
-11.5153
96.6708
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
2 - 43
2
X-RAY DIFFRACTION
2
A
44 - 75
3
X-RAY DIFFRACTION
3
A
76 - 111
4
X-RAY DIFFRACTION
4
A
112 - 144
5
X-RAY DIFFRACTION
5
B
3 - 46
6
X-RAY DIFFRACTION
6
B
47 - 78
7
X-RAY DIFFRACTION
7
B
79 - 119
8
X-RAY DIFFRACTION
8
B
120 - 144
9
X-RAY DIFFRACTION
9
C
4 - 36
10
X-RAY DIFFRACTION
10
C
37 - 108
11
X-RAY DIFFRACTION
11
C
109 - 119
12
X-RAY DIFFRACTION
12
C
120 - 144
13
X-RAY DIFFRACTION
13
D
2 - 78
14
X-RAY DIFFRACTION
14
D
79 - 112
15
X-RAY DIFFRACTION
15
D
113 - 130
16
X-RAY DIFFRACTION
16
D
131 - 144
+
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