Utilization of Ketone Bodies / 3-oxoacid CoA-transferase / cellular ketone body metabolic process / succinyl-CoA:3-oxo-acid CoA-transferase activity / ketone catabolic process / CoA-transferase activity / ketone body catabolic process / response to xenobiotic stimulus => GO:0009410 / response to starvation / positive regulation of insulin secretion involved in cellular response to glucose stimulus ...Utilization of Ketone Bodies / 3-oxoacid CoA-transferase / cellular ketone body metabolic process / succinyl-CoA:3-oxo-acid CoA-transferase activity / ketone catabolic process / CoA-transferase activity / ketone body catabolic process / response to xenobiotic stimulus => GO:0009410 / response to starvation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / adipose tissue development / response to nutrient / response to hormone / response to activity / brain development / heart development / response to ethanol / mitochondrial matrix / mitochondrion / nucleoplasm / identical protein binding Similarity search - Function
3-oxoacid CoA-transferase, subunit A / Coenzyme A transferase active site / 3-oxoacid CoA-transferase, subunit B / 3-oxoacid CoA-transferase / Coenzyme A transferases signature 2. / Coenzyme A transferase binding site / Coenzyme A transferases signature 1. / Glutaconate Coenzyme A-transferase / Glutaconate Coenzyme A-transferase / Coenzyme A transferase family I ...3-oxoacid CoA-transferase, subunit A / Coenzyme A transferase active site / 3-oxoacid CoA-transferase, subunit B / 3-oxoacid CoA-transferase / Coenzyme A transferases signature 2. / Coenzyme A transferase binding site / Coenzyme A transferases signature 1. / Glutaconate Coenzyme A-transferase / Glutaconate Coenzyme A-transferase / Coenzyme A transferase family I / Coenzyme A transferase / Coenzyme A transferase / NagB/RpiA transferase-like / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology
Resolution: 2.2→48.11 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 12.701 / SU ML: 0.16 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.257 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Extra density in the active site could not be interpreted and was left unmodelled.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22473
1302
1.4 %
RANDOM
Rwork
0.17821
-
-
-
all
0.17887
90754
-
-
obs
0.17887
90754
98.41 %
-
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: 29.557 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.11 Å2
0 Å2
-1.34 Å2
2-
-
0.48 Å2
0 Å2
3-
-
-
-1.33 Å2
Refinement step
Cycle: LAST / Resolution: 2.2→48.11 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
13833
0
12
375
14220
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.016
0.022
14093
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
9361
X-RAY DIFFRACTION
r_angle_refined_deg
1.556
1.969
19096
X-RAY DIFFRACTION
r_angle_other_deg
0.966
3
22940
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.987
5
1852
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
38.75
24.432
555
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.143
15
2317
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.154
15
75
X-RAY DIFFRACTION
r_chiral_restr
0.09
0.2
2207
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
15857
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
2726
X-RAY DIFFRACTION
r_nbd_refined
0.191
0.2
2519
X-RAY DIFFRACTION
r_nbd_other
0.197
0.2
9848
X-RAY DIFFRACTION
r_nbtor_refined
0.172
0.2
6709
X-RAY DIFFRACTION
r_nbtor_other
0.087
0.2
7603
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.158
0.2
523
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.263
0.2
7
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.185
0.2
28
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.097
0.2
3
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
0.711
1.5
9484
X-RAY DIFFRACTION
r_mcbond_other
0.168
1.5
3826
X-RAY DIFFRACTION
r_mcangle_it
1.099
2
14677
X-RAY DIFFRACTION
r_scbond_it
1.93
3
5233
X-RAY DIFFRACTION
r_scangle_it
2.898
4.5
4418
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.2→2.257 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.342
86
-
Rwork
0.234
6472
-
obs
-
-
94.76 %
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
1.2579
0.2119
0.3355
1.3094
-0.1649
2.4639
-0.0032
0.1396
-0.1217
-0.109
0.1136
-0.1018
0.1857
0.1064
-0.1104
-0.1872
0.0591
0.0061
-0.1287
-0.0372
-0.2202
26.4793
37.201
-1.4549
2
3.658
-0.0471
1.0204
2.921
-1.0016
2.2526
0.1378
-0.0893
-0.6013
0.0828
0.1551
0.4026
0.592
-0.5336
-0.293
0.0482
-0.1022
-0.0064
0.0668
0.0701
-0.0257
7.963
19.5373
14.3289
3
0.8508
0.3663
0.3383
1.6468
0.4152
2.4056
-0.1166
-0.095
0.2793
0.0019
-0.0086
0.3179
-0.5431
-0.5926
0.1252
-0.0223
0.2194
-0.0143
0.0424
-0.029
-0.091
8.7486
60.4661
9.5129
4
2.2236
0.9615
-0.0976
2.8012
0.6224
3.2077
-0.0613
-0.0421
0.5624
-0.1722
0.2238
-0.162
-0.8393
0.4163
-0.1625
0.3213
-0.0539
-0.0405
-0.0686
-0.0854
0.0591
34.3257
76.7309
6.6061
5
1.5031
-0.3852
0.4222
1.7258
-0.1282
1.8685
0.1126
-0.0483
0.1117
-0.0275
-0.0401
-0.4219
-0.0687
0.2043
-0.0725
-0.2349
-0.0155
0.0254
-0.1732
0.0133
-0.1191
46.607
35.766
47.9422
6
2.3786
-0.9254
-0.487
4.0243
-2.1332
4.2166
0.1087
-0.2394
0.3382
0.4748
0.2643
0.486
-0.6763
-0.2883
-0.373
-0.1217
0.0428
0.1078
-0.1263
0.0029
-0.0801
21.0449
51.2478
50.1605
7
1.5895
-0.0955
0.0758
2.051
0.212
1.938
0.1661
-0.2452
-0.4926
0.05
-0.0511
0.1937
0.4893
-0.2416
-0.115
-0.053
-0.0975
-0.1107
-0.1424
0.1221
-0.0214
28.3816
10.7824
52.293
8
5.9308
0.1265
2.6226
3.4935
1.06
3.061
0.3373
0.6805
-1.2024
-0.3315
0.1161
-0.422
0.7139
0.5347
-0.4534
0.2455
0.1018
-0.116
-0.0475
-0.0955
0.3118
47.923
-3.5739
36.9749
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
40 - 297
2 - 259
2
X-RAY DIFFRACTION
1
A
A
342 - 393
304 - 355
3
X-RAY DIFFRACTION
2
A
A
298 - 341
260 - 303
4
X-RAY DIFFRACTION
2
A
A
394 - 519
356 - 481
5
X-RAY DIFFRACTION
3
B
B
40 - 285
2 - 247
6
X-RAY DIFFRACTION
3
B
B
342 - 393
304 - 355
7
X-RAY DIFFRACTION
4
B
B
299 - 341
261 - 303
8
X-RAY DIFFRACTION
4
B
B
394 - 518
356 - 480
9
X-RAY DIFFRACTION
5
C
C
40 - 285
2 - 247
10
X-RAY DIFFRACTION
5
C
C
342 - 393
304 - 355
11
X-RAY DIFFRACTION
6
C
C
299 - 341
261 - 303
12
X-RAY DIFFRACTION
6
C
C
394 - 519
356 - 481
13
X-RAY DIFFRACTION
7
D
D
40 - 286
2 - 248
14
X-RAY DIFFRACTION
7
D
D
342 - 393
304 - 355
15
X-RAY DIFFRACTION
8
D
D
302 - 341
264 - 303
16
X-RAY DIFFRACTION
8
D
D
394 - 519
356 - 481
+
About Yorodumi
-
News
-
Feb 9, 2022. New format data for meta-information of EMDB entries
New format data for meta-information of EMDB entries
Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi