- PDB-8ru5: ATPase family AAA domain containing 2 with crystallization epitop... -
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Basic information
Entry
Database: PDB / ID: 8ru5
Title
ATPase family AAA domain containing 2 with crystallization epitope mutations V1022R:Q1027E
Components
ATPase family AAA domain-containing protein 2
Keywords
SIGNALING PROTEIN / Crystal Epitopes / Bromodomain
Function / homology
Function and homology information
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
ATPasefamilyAAAdomain-containingprotein2 / AAA nuclear coregulator cancer-associated protein / ANCCA
Mass: 15512.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ATAD2, L16, PRO2000 / Production host: Escherichia coli (E. coli) References: UniProt: Q6PL18, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→41.047 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.963 / Cross valid method: FREE R-VALUE / ESU R: 0.065 / ESU R Free: 0.062 Details: Hydrogens have been used if present in the input file
Rfactor
Num. reflection
% reflection
Rfree
0.2214
1573
4.93 %
Rwork
0.2109
30335
-
all
0.211
-
-
obs
-
31908
98.251 %
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: 29.255 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.625 Å2
0 Å2
0 Å2
2-
-
-0.565 Å2
-0 Å2
3-
-
-
-1.061 Å2
Refinement step
Cycle: LAST / Resolution: 1.36→41.047 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1043
0
8
132
1183
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.01
0.012
1118
X-RAY DIFFRACTION
r_angle_refined_deg
1.546
1.86
1519
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.757
5
139
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
1.141
5
15
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.241
10
187
X-RAY DIFFRACTION
r_dihedral_angle_6_deg
17.971
10
59
X-RAY DIFFRACTION
r_chiral_restr
0.084
0.2
171
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
857
X-RAY DIFFRACTION
r_nbd_refined
0.215
0.2
529
X-RAY DIFFRACTION
r_nbtor_refined
0.321
0.2
792
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.281
0.2
86
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.169
0.2
19
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.255
0.2
10
X-RAY DIFFRACTION
r_mcbond_it
1.388
2.641
544
X-RAY DIFFRACTION
r_mcangle_it
2.26
4.735
687
X-RAY DIFFRACTION
r_scbond_it
2.399
2.989
574
X-RAY DIFFRACTION
r_scangle_it
3.979
5.337
832
X-RAY DIFFRACTION
r_lrange_it
5.739
32.686
1788
LS refinement shell
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Rfactor all
Num. reflection all
Fsc free
Fsc work
% reflection obs (%)
WRfactor Rwork
1.36-1.395
0.335
107
0.337
2087
0.337
2358
0.923
0.908
93.045
0.324
1.395-1.433
0.362
121
0.331
2076
0.333
2306
0.902
0.917
95.2732
0.311
1.433-1.475
0.321
112
0.3
2066
0.301
2228
0.921
0.935
97.7558
0.273
1.475-1.52
0.26
99
0.243
2036
0.244
2165
0.951
0.956
98.6143
0.211
1.52-1.57
0.257
84
0.237
2025
0.238
2120
0.954
0.961
99.4811
0.205
1.57-1.625
0.217
111
0.227
1930
0.227
2049
0.966
0.966
99.6096
0.198
1.625-1.686
0.234
105
0.224
1854
0.225
1987
0.965
0.966
98.5908
0.195
1.686-1.755
0.233
102
0.214
1808
0.215
1918
0.963
0.97
99.5829
0.188
1.755-1.833
0.268
95
0.216
1744
0.219
1850
0.953
0.969
99.4054
0.194
1.833-1.922
0.251
85
0.222
1657
0.223
1751
0.96
0.968
99.486
0.204
1.922-2.026
0.263
75
0.211
1573
0.213
1664
0.95
0.971
99.0385
0.199
2.026-2.149
0.217
82
0.21
1491
0.211
1587
0.972
0.975
99.1178
0.206
2.149-2.297
0.208
67
0.202
1412
0.202
1494
0.98
0.975
98.996
0.199
2.297-2.48
0.237
72
0.191
1304
0.193
1397
0.971
0.976
98.4968
0.198
2.48-2.716
0.158
51
0.213
1245
0.211
1305
0.983
0.971
99.3103
0.223
2.716-3.034
0.246
51
0.207
1124
0.208
1180
0.963
0.974
99.5763
0.23
3.034-3.501
0.238
55
0.2
984
0.202
1049
0.96
0.974
99.0467
0.229
3.501-4.28
0.151
46
0.174
847
0.173
910
0.987
0.981
98.1319
0.208
4.28-6.02
0.247
38
0.205
655
0.207
717
0.969
0.975
96.6527
0.266
6.02-41.047
0.177
15
0.251
417
0.248
441
0.978
0.964
97.9592
0.321
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