Heme-binding protein/Heme-binding protein / cytochrome / sulfur oxidation pathway / Heme-binding protein-Heme-binding protein complex
Function / homology
Function and homology information
L-cysteine S-thiosulfotransferase / oxidoreductase activity, acting on a sulfur group of donors, cytochrome as acceptor / sulfur oxidation / sulfurtransferase activity / cytochrome complex / thiosulfate sulfurtransferase activity / periplasmic space / oxidoreductase activity / electron transfer activity / iron ion binding ...L-cysteine S-thiosulfotransferase / oxidoreductase activity, acting on a sulfur group of donors, cytochrome as acceptor / sulfur oxidation / sulfurtransferase activity / cytochrome complex / thiosulfate sulfurtransferase activity / periplasmic space / oxidoreductase activity / electron transfer activity / iron ion binding / copper ion binding / protein heterodimerization activity / heme binding / metal ion binding Similarity search - Function
Sulfur oxidation c-type cytochrome SoxX, type II / L-cysteine S-thiosulfotransferase subunit SoxA / Sulfur oxidation c-type cytochrome SoxX / SoxA/TsdA, cytochrome c domain / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily ...Sulfur oxidation c-type cytochrome SoxX, type II / L-cysteine S-thiosulfotransferase subunit SoxA / Sulfur oxidation c-type cytochrome SoxX / SoxA/TsdA, cytochrome c domain / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha Similarity search - Domain/homology
Method to determine structure: MAD / Resolution: 1.77→35.31 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.951 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23044
5553
5 %
RANDOM
Rwork
0.18292
-
-
-
obs
0.18529
105300
92.22 %
-
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: 29.955 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.82 Å2
0.14 Å2
-0.08 Å2
2-
-
0.13 Å2
0.25 Å2
3-
-
-
0.89 Å2
Refinement step
Cycle: LAST / Resolution: 1.77→35.31 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
9420
0
263
833
10516
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.014
0.022
10028
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.454
2.049
13697
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.366
5
1254
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.318
23.882
425
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.616
15
1635
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.762
15
76
X-RAY DIFFRACTION
r_chiral_restr
0.097
0.2
1432
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
7730
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.244
0.2
5088
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.306
0.2
6888
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.162
0.2
766
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
0.006
0.2
1
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.21
0.2
80
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.204
0.2
22
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
0.889
1.5
6307
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.378
2
9925
X-RAY DIFFRACTION
r_scbond_it
2.533
3
4285
X-RAY DIFFRACTION
r_scangle_it
3.967
4.5
3746
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.771→1.817 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.275
357
-
Rwork
0.215
6377
-
obs
-
-
76.01 %
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
1.9138
-0.2512
0.8459
0.5044
-0.1585
1.0401
0.0958
-0.1094
-0.2232
-0.0359
0.0083
0.0704
0.0399
-0.1996
-0.1041
-0.0538
0.0088
0.0013
-0.0217
0.0092
-0.0615
-42.8121
14.6504
16.7044
2
1.4108
-0.2345
1.0264
0.7346
-0.2488
0.7555
0.0349
0.0296
-0.1304
-0.0392
0.0036
-0.0105
0.0577
-0.0372
-0.0386
-0.0203
0.0231
-0.0129
-0.0104
-0.0166
-0.0531
-34.9297
15.8918
14.8682
3
2.0191
0.7793
1.6912
0.9661
0.3536
1.8593
0.1286
-0.245
-0.1755
0.0302
0.0045
-0.0014
0.246
-0.0592
-0.1331
0.022
-0.0047
-0.0059
-0.0536
0.0434
-0.0379
-23.4854
9.1882
32.9542
4
2.1114
-0.2028
-0.1031
0.5977
-0.1951
1.0531
0.0419
0.1905
-0.0508
0.0138
-0.0164
-0.0435
0.0612
0.1552
-0.0255
-0.0564
0.02
0.0068
-0.0063
0.01
-0.0593
-3.9276
14.0304
18.7621
5
1.4807
0.4711
-0.2524
1.0363
-0.1529
0.5105
0.0281
-0.0889
0.0638
-0.037
0.028
0.1612
-0.011
-0.0618
-0.0561
-0.0317
0.0111
-0.021
-0.046
0.0373
-0.0756
-41.9302
12.2985
60.4467
6
0.7759
0.4396
-0.146
1.4285
0.2398
0.5487
0.0361
-0.0159
-0.0215
-0.0296
0.006
0.0201
0.0111
-0.0226
-0.0421
-0.0156
-0.0148
-0.0166
-0.0167
0.0421
-0.0657
-34.0004
10.2207
60.3148
7
1.3195
0.6396
-0.2427
0.8072
-0.3919
1.1043
0.1585
-0.0749
0.2969
0.0793
-0.037
0.0492
-0.1978
-0.0067
-0.1215
0.0221
0.0048
0.0174
-0.0611
-0.0155
-0.0465
-22.6936
29.3153
57.584
8
2.4368
-0.0164
0.0392
1.1038
-0.1048
0.6653
-0.0056
-0.1638
-0.1955
0.1209
-0.0259
-0.1295
-0.0318
0.067
0.0315
-0.0432
0.0002
-0.0185
-0.0465
0.0378
-0.0372
-3.1458
14.4647
60.0649
9
2.3924
-0.9398
-0.9576
0.8788
0.6884
1.5086
0.1552
0.3599
0.0062
-0.0417
-0.2334
0.174
-0.0388
-0.3221
0.0782
-0.0384
0.0022
0.0036
-0.0413
-0.0133
-0.0419
-40.7291
51.5766
40.983
10
1.8906
-1.0542
-0.7818
0.6578
0.7332
1.5864
0.0512
0.0614
0.1442
-0.066
-0.042
0.1179
-0.0095
-0.0267
-0.0092
0.0077
0.0058
0.0336
-0.0743
-0.0065
-0.0166
-32.8828
52.6527
43.215
11
2.4407
-1.8738
-0.2866
3.2138
-0.0591
0.7198
0.1204
0.2956
-0.0337
-0.2812
-0.134
-0.0309
-0.0878
-0.0222
0.0136
0.0602
0.0079
-0.0059
-0.0446
0.0057
-0.1157
-21.6598
41.5543
27.5973
12
2.934
0.3552
-0.1349
1.2643
0.4148
1.4091
-0.0032
-0.0473
0.2095
-0.1186
0.1087
-0.2277
-0.0799
0.1618
-0.1054
-0.0568
-0.0229
0.022
-0.0538
-0.0263
-0.0296
-2.018
49.8617
39.4973
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
47 - 211
2
X-RAY DIFFRACTION
2
A
212 - 274
3
X-RAY DIFFRACTION
3
B
31 - 81
4
X-RAY DIFFRACTION
4
B
82 - 208
5
X-RAY DIFFRACTION
5
C
47 - 211
6
X-RAY DIFFRACTION
6
C
212 - 274
7
X-RAY DIFFRACTION
7
D
31 - 81
8
X-RAY DIFFRACTION
8
D
82 - 208
9
X-RAY DIFFRACTION
9
E
47 - 211
10
X-RAY DIFFRACTION
10
E
212 - 274
11
X-RAY DIFFRACTION
11
F
31 - 81
12
X-RAY DIFFRACTION
12
F
82 - 208
+
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