Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / histone binding / chromatin binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / ATP binding / nucleus Similarity search - Function
ATPase family AAA domain-containing protein ATAD2-like / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Bromodomain / Bromodomain profile. / bromo domain ...ATPase family AAA domain-containing protein ATAD2-like / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase Similarity search - Domain/homology
Resolution: 2.18→38.322 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.907 / SU B: 5.151 / SU ML: 0.125 / Cross valid method: FREE R-VALUE / ESU R: 0.181 / ESU R Free: 0.171 Details: Hydrogens have been used if present in the input file
Rfactor
Num. reflection
% reflection
Rfree
0.2461
665
4.987 %
Rwork
0.2064
12670
-
all
0.208
-
-
obs
-
13335
94.387 %
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parameters
Biso mean: 32.33 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.042 Å2
0.021 Å2
-0 Å2
2-
-
0.042 Å2
0 Å2
3-
-
-
-0.136 Å2
Refinement step
Cycle: LAST / Resolution: 2.18→38.322 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1069
0
29
96
1194
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.008
0.012
1113
X-RAY DIFFRACTION
r_angle_refined_deg
1.769
1.655
1499
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.841
5
127
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
30.554
21.216
74
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
18.251
15
204
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
18.563
15
13
X-RAY DIFFRACTION
r_chiral_restr
0.118
0.2
144
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
842
X-RAY DIFFRACTION
r_nbd_refined
0.232
0.2
556
X-RAY DIFFRACTION
r_nbtor_refined
0.327
0.2
774
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.185
0.2
88
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.282
0.2
33
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.181
0.2
11
X-RAY DIFFRACTION
r_mcbond_it
2.491
2.932
511
X-RAY DIFFRACTION
r_mcangle_it
3.53
4.38
637
X-RAY DIFFRACTION
r_scbond_it
4.348
3.338
602
X-RAY DIFFRACTION
r_scangle_it
6.529
4.834
862
X-RAY DIFFRACTION
r_lrange_it
8.245
40.323
1775
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.18-2.237
0.303
38
0.259
790
X-RAY DIFFRACTION
81.097
2.237-2.298
0.31
39
0.252
930
X-RAY DIFFRACTION
98.1763
2.298-2.365
0.279
44
0.244
896
X-RAY DIFFRACTION
98.3264
2.365-2.438
0.277
40
0.247
882
X-RAY DIFFRACTION
98.0851
2.438-2.518
0.255
38
0.238
857
X-RAY DIFFRACTION
98.3516
2.518-2.606
0.334
50
0.245
815
X-RAY DIFFRACTION
97.5197
2.606-2.704
0.234
48
0.221
778
X-RAY DIFFRACTION
95.1613
2.704-2.815
0.283
34
0.2
735
X-RAY DIFFRACTION
95.0556
2.815-2.94
0.202
38
0.21
709
X-RAY DIFFRACTION
93.375
2.94-3.083
0.248
35
0.241
659
X-RAY DIFFRACTION
91.7989
3.083-3.25
0.365
34
0.225
644
X-RAY DIFFRACTION
93.1319
3.25-3.447
0.255
41
0.228
620
X-RAY DIFFRACTION
94.2939
3.447-3.685
0.23
35
0.203
567
X-RAY DIFFRACTION
93.1889
3.685-3.98
0.194
30
0.173
566
X-RAY DIFFRACTION
95.36
3.98-4.359
0.253
29
0.157
498
X-RAY DIFFRACTION
95.1264
4.359-4.873
0.221
31
0.147
472
X-RAY DIFFRACTION
95.6274
4.873-5.626
0.192
21
0.155
424
X-RAY DIFFRACTION
95.0855
5.626-6.888
0.195
13
0.201
369
X-RAY DIFFRACTION
94.321
6.888-9.728
0.184
20
0.171
293
X-RAY DIFFRACTION
94.8485
9.728-38.322
0.206
7
0.245
166
X-RAY DIFFRACTION
81.9905
+
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