The asymmetric contains 6 monomers. Four monomers (chains C,D,E,F) form one complete tetramer. Two monomers (chains A,B) form tetramer by rotation around the diagonal 2-fold in the ab plane at z=1/4 (symmop 8 of the spacegroup: -y,-x,-z+1/2), followed by 0,0,-1 translation
Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal grow
Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 2-4 microlitre of protein solution (5-15 mg/ml, 100 micromolar ThDP, 10 micromolar FAD, 1mM MgCl2 and 10 mM quinone Q0) were mixed with equal volume of reservoir solution (0.5% PEG6000, 0.5M ...Details: 2-4 microlitre of protein solution (5-15 mg/ml, 100 micromolar ThDP, 10 micromolar FAD, 1mM MgCl2 and 10 mM quinone Q0) were mixed with equal volume of reservoir solution (0.5% PEG6000, 0.5M NaCl, 40 mM DTT), pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 294.K
Av σ(I) over netI: 8.92 / Number: 1046103 / Rmerge(I) obs: 0.127 / D res high: 2.8 Å / Num. obs: 210109 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
% possible obs (%)
ID
Rmerge(I) obs
10
50
90.8
1
0.032
8
10
100
1
0.037
6
8
100
1
0.056
5
6
100
1
0.072
3
5
100
1
0.145
2.8
3
100
1
0.573
Reflection
Resolution: 2.7→50 Å / Num. obs: 122672 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 37.8 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.089 / Net I/σ(I): 9.43
Reflection shell
Resolution: 2.7→2.8 Å / Redundancy: 2.21 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 2.76 / Rsym value: 0.28 / % possible all: 93.1
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
XSCALE
datascaling
SHARP
phasing
SOLOMON
phasing
REFMAC
refinement
PDB_EXTRACT
2
dataextraction
XDS
datareduction
Refinement
Method to determine structure: MAD / Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 25.351 / SU ML: 0.255 / Cross valid method: THROUGHOUT / ESU R Free: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.253
2453
2 %
RANDOM
Rwork
0.219
-
-
-
obs
0.22
122207
99.9 %
-
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: 27.79 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.09 Å2
0 Å2
0 Å2
2-
-
-0.09 Å2
0 Å2
3-
-
-
0.18 Å2
Refinement step
Cycle: LAST / Resolution: 2.7→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
27180
0
548
363
28091
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.009
0.022
28299
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
26036
X-RAY DIFFRACTION
r_angle_refined_deg
1.229
1.98
38480
X-RAY DIFFRACTION
r_angle_other_deg
0.79
3
60354
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.916
5
3546
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.25
23.99
1218
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.993
15
4590
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.681
15
192
X-RAY DIFFRACTION
r_chiral_restr
0.064
0.2
4326
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.02
31473
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
5521
X-RAY DIFFRACTION
r_nbd_refined
0.184
0.2
5719
X-RAY DIFFRACTION
r_nbd_other
0.169
0.2
26431
X-RAY DIFFRACTION
r_nbtor_refined
0.17
0.2
13578
X-RAY DIFFRACTION
r_nbtor_other
0.081
0.2
16561
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.127
0.2
529
X-RAY DIFFRACTION
r_xyhbond_nbd_other
0.02
0.2
1
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.19
0.2
58
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.198
0.2
230
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.164
0.2
15
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
0.524
1.5
22193
X-RAY DIFFRACTION
r_mcbond_other
0.065
1.5
7194
X-RAY DIFFRACTION
r_mcangle_it
0.504
2
28440
X-RAY DIFFRACTION
r_scbond_it
1.024
3
12070
X-RAY DIFFRACTION
r_scangle_it
1.463
4.5
10040
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
Refine LS restraints NCS
Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
Dom-ID
Auth asym-ID
Number
Type
Rms dev position (Å)
Weight position
1
A
3470
tightpositional
0.02
0.05
2
B
3470
tightpositional
0.02
0.05
3
C
3470
tightpositional
0.02
0.05
4
D
3470
tightpositional
0.02
0.05
5
E
3470
tightpositional
0.02
0.05
6
F
3470
tightpositional
0.02
0.05
1
A
5334
mediumpositional
0.31
0.5
2
B
5334
mediumpositional
0.27
0.5
3
C
5334
mediumpositional
0.29
0.5
4
D
5334
mediumpositional
0.27
0.5
5
E
5334
mediumpositional
0.3
0.5
6
F
5334
mediumpositional
0.34
0.5
1
A
3470
tightthermal
0.04
0.5
2
B
3470
tightthermal
0.03
0.5
3
C
3470
tightthermal
0.03
0.5
4
D
3470
tightthermal
0.03
0.5
5
E
3470
tightthermal
0.03
0.5
6
F
3470
tightthermal
0.03
0.5
1
A
5334
mediumthermal
0.21
2
2
B
5334
mediumthermal
0.2
2
3
C
5334
mediumthermal
0.16
2
4
D
5334
mediumthermal
0.15
2
5
E
5334
mediumthermal
0.14
2
6
F
5334
mediumthermal
0.15
2
LS refinement shell
Resolution: 2.7→2.77 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.357
180
-
Rwork
0.328
7745
-
obs
-
-
98.76 %
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
0.5151
0.0719
0.2888
0.4086
0.1416
1.1767
-0.0199
0.0692
0.0733
-0.0565
-0.0134
-0.0318
-0.1155
0.0315
0.0333
-0.0066
-0.0175
-0.0016
0.0132
0.0224
0.0369
-30.1887
54.9803
-63.4111
2
0.2684
-0.0308
-0.0356
0.4982
0.1904
0.4954
-0.0182
-0.0784
0.0105
0.0866
-0.0074
-0.0232
-0.0117
0.051
0.0256
-0.0018
-0.0209
-0.0333
0.0263
0.0161
0.0178
-24.0709
42.0087
-41.9667
3
0.3579
-0.0934
-0.2855
1.4183
0.8586
1.9284
0.0505
-0.0968
-0.0617
0.2116
0.0376
-0.1523
0.0514
0.1922
-0.0881
-0.0507
0.0096
-0.0991
-0.0203
0.0252
0.0031
-17.1728
33.1415
-39.5649
4
0.5387
0.2175
-0.2215
0.68
-0.4315
0.6249
0.0141
-0.0691
0.0071
0.0719
-0.0196
-0.0645
-0.0597
0.06
0.0054
0.045
-0.0312
-0.0167
-0.0021
-0.0045
0.0418
-49.9455
72.5459
-55.1037
5
0.4013
-0.0571
-0.1165
0.4712
-0.178
0.5309
0.0543
0.104
0.0835
-0.0167
-0.0203
-0.017
-0.1185
-0.015
-0.034
0.0441
-0.0186
0.0242
-0.0049
0.0456
0.0388
-57.3004
84.3637
-76.8324
6
2.0993
0.187
-1.635
0.536
-0.3466
1.7987
0.121
0.1539
0.2803
0.0765
0.0971
0.1582
-0.1725
-0.0104
-0.218
0.0231
0.054
0.0104
-0.0618
0.1016
0.035
-65.4942
91.9776
-79.5028
7
0.691
0.0227
0.2858
0.443
0.0601
1.1467
0.0086
0.1227
0.035
-0.1171
-0.032
-0.0261
-0.1283
0.0085
0.0234
0.2248
-0.0145
0.0308
0.1361
0.0154
0.1569
-30.0168
55.005
-139.1008
8
0.26
-0.0175
-0.0392
0.4787
0.1477
0.4607
0.0122
-0.0545
-0.0292
0.0643
-0.0269
-0.044
-0.015
0.0391
0.0147
0.1978
-0.0316
-0.0043
0.1425
0.022
0.1412
-23.9558
42.0608
-117.616
9
0.5788
-0.1967
-0.2936
1.4227
0.3933
1.6396
0.1037
0.0369
-0.0122
0.2537
-0.0139
-0.1471
0.081
0.125
-0.0898
0.1847
-0.034
-0.0492
0.1104
0.0288
0.1174
-17.0873
33.1984
-115.1904
10
0.6585
0.2334
-0.2635
0.8463
-0.4527
0.8197
-0.0205
-0.0253
-0.0098
0.0834
-0.0112
-0.0474
0.0141
0.0598
0.0317
0.2301
-0.0198
0.0136
0.1107
0.0036
0.163
-49.7203
72.5299
-130.6967
11
0.6352
-0.2076
-0.0087
0.5899
-0.0693
0.5385
0.0536
0.1678
0.0465
-0.0757
-0.0886
0.0013
-0.0548
0.0126
0.035
0.2183
-0.0078
0.0291
0.1492
0.0219
0.1452
-57.1707
84.4159
-152.3423
12
1.7753
-0.0294
-1.4986
0.05
-0.002
2.4105
0.1478
0.2619
0.2179
-0.0149
-0.0401
0.0023
-0.0453
0.0151
-0.1077
0.1986
0.0518
0.0072
0.0849
0.0417
0.1473
-65.3091
92.0588
-154.9233
13
0.4265
0.0142
0.1505
0.5166
0.2181
1.5946
0.0175
0.0063
-0.0965
-0.009
-0.0356
0.1665
0.0339
-0.1948
0.0182
0.2296
-0.0199
0.022
0.1286
-0.0468
0.2501
-54.886
30.3071
-136.9616
14
0.5397
-0.0997
0.0445
0.298
0.0128
0.53
0.0431
0.1916
-0.1014
-0.0972
-0.0736
0.076
0.079
-0.0248
0.0305
0.2808
0.0017
0.0127
0.1822
-0.0875
0.219
-41.8964
24.1179
-158.3733
15
1.5122
-0.3379
0.9861
0.6142
-0.1781
1.8458
0.1184
0.3794
-0.2461
-0.0934
-0.0079
0.0412
0.2297
0.0605
-0.1105
0.2363
0.0538
0.0428
0.1652
-0.1238
0.1965
-33.0601
17.1792
-160.7607
16
0.8203
0.1564
-0.2578
0.5605
-0.1802
0.5566
0.0298
0.1069
-0.105
-0.1559
-0.013
0.0433
0.1322
-0.0149
-0.0168
0.243
-0.0353
0.0147
0.1949
-0.0596
0.2362
-72.5751
50.1339
-145.1222
17
0.2903
0.1154
-0.1071
0.8257
-0.2687
0.6926
0.005
-0.0559
-0.0768
0.0985
0.0229
0.1331
0.0175
-0.1531
-0.0279
0.1818
-0.0384
0.0728
0.2079
-0.0057
0.228
-84.2287
57.4499
-123.2812
18
0.9982
-0.0608
-0.404
2.0701
-1.0714
1.5154
0.0577
0.0347
0.0892
0.2062
0.03
0.2906
0.0521
-0.268
-0.0878
0.1609
-0.0239
0.1349
0.1571
-0.0108
0.2395
-91.7746
65.6578
-120.4737
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
2 - 233
25 - 256
2
X-RAY DIFFRACTION
2
A
A
234 - 530
257 - 553
3
X-RAY DIFFRACTION
3
A
A
531 - 593
554 - 616
4
X-RAY DIFFRACTION
4
B
B
2 - 233
25 - 256
5
X-RAY DIFFRACTION
5
B
B
234 - 530
257 - 553
6
X-RAY DIFFRACTION
6
B
B
531 - 593
554 - 616
7
X-RAY DIFFRACTION
7
C
C
2 - 233
25 - 256
8
X-RAY DIFFRACTION
8
C
C
234 - 530
257 - 553
9
X-RAY DIFFRACTION
9
C
C
531 - 593
554 - 616
10
X-RAY DIFFRACTION
10
D
D
2 - 233
25 - 256
11
X-RAY DIFFRACTION
11
D
D
234 - 530
257 - 553
12
X-RAY DIFFRACTION
12
D
D
531 - 593
554 - 616
13
X-RAY DIFFRACTION
13
E
E
2 - 233
25 - 256
14
X-RAY DIFFRACTION
14
E
E
234 - 530
257 - 553
15
X-RAY DIFFRACTION
15
E
E
531 - 593
554 - 616
16
X-RAY DIFFRACTION
16
F
F
2 - 233
25 - 256
17
X-RAY DIFFRACTION
17
F
F
234 - 530
257 - 553
18
X-RAY DIFFRACTION
18
F
F
531 - 593
554 - 616
+
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