protein unfolding / cellular response to heat / protein refolding / ATP hydrolysis activity / ATP binding / identical protein binding / cytoplasm Similarity search - Function
Chaperonin ClpB / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / : / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / Clp repeat (R) domain profile. ...Chaperonin ClpB / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / : / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / Clp repeat (R) domain profile. / Clp, repeat (R) domain / Clp, N-terminal domain superfamily / Helicase, Ruva Protein; domain 3 - #60 / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
Resolution: 2.8→49.38 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.891 / SU B: 41.748 / SU ML: 0.383 / Cross valid method: THROUGHOUT / ESU R Free: 0.445 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.29484
1380
5 %
RANDOM
Rwork
0.24048
-
-
-
all
0.24315
26218
-
-
obs
0.24315
26218
100 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 68.744 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-3.79 Å2
0 Å2
0 Å2
2-
-
0.68 Å2
0 Å2
3-
-
-
3.11 Å2
Refinement step
Cycle: LAST / Resolution: 2.8→49.38 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
7167
0
123
0
7290
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.006
0.022
7419
X-RAY DIFFRACTION
r_angle_refined_deg
0.974
2.007
10048
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.312
5
897
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.391
22.881
354
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.377
15
1314
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
13.188
15
88
X-RAY DIFFRACTION
r_chiral_restr
0.059
0.2
1128
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.021
5612
X-RAY DIFFRACTION
r_mcbond_it
0.078
1.5
4477
X-RAY DIFFRACTION
r_mcangle_it
0.169
2
7233
X-RAY DIFFRACTION
r_scbond_it
0.352
3
2942
X-RAY DIFFRACTION
r_scangle_it
0.657
4.5
2815
LS refinement shell
Resolution: 2.8→2.872 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.431
101
-
Rwork
0.357
1924
-
obs
-
-
100 %
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
6.892
0.7084
2.1645
1.4227
1.0568
2.456
-0.2047
-0.0468
0.3315
0.0068
0.0932
-0.3792
0.0357
0.1959
0.1115
0.0466
-0.01
0.0034
0.1309
0.0061
0.1989
4.767
-20.5988
-22.5142
2
18.5251
6.137
7.1066
7.9939
-5.4132
12.9806
-0.6056
2.0119
-0.2864
-0.5056
0.2461
-0.5358
0.0311
1.0463
0.3595
0.2911
0.1958
0.1954
0.7147
0.1336
0.232
-4.4212
-15.452
-42.359
3
5.5863
0.1579
-3.9521
0.6564
0.8842
6.4227
0.0298
-0.0519
0.289
0.1308
-0.0697
0.0166
-0.0501
-0.1204
0.0399
0.0679
0.0163
-0.0637
0.1724
-0.0636
0.1425
-26.5997
-15.3261
-14.073
4
4.0112
-1.9548
1.5278
4.5292
-1.7365
2.8164
-0.0208
-0.1442
-0.1513
-0.008
-0.053
-0.088
0.0027
0.07
0.0738
0.1067
0.0372
-0.0903
0.197
-0.0961
0.1341
-6.2062
-7.8229
6.3434
5
14.1787
-11.6022
4.2889
15.5743
-6.9282
11.5667
0.3857
0.7563
0.6592
-1.6127
-0.6122
-1.5173
-0.3629
0.4426
0.2265
0.652
0.1144
0.1707
0.4221
0.0058
0.3258
-4.3214
2.1132
-13.1441
6
1.112
-1.6164
-0.1243
5.1286
3.3828
9.4405
0.1592
-0.2681
0.3613
-0.2835
0.0182
-0.231
-0.5818
-0.3975
-0.1774
0.2322
0.0146
-0.1373
0.2715
-0.1047
0.6523
-13.6699
25.1706
12.2293
7
4.9402
-0.559
-0.3693
3.279
-0.5402
5.1497
0.2372
0.5604
0.5996
-0.3211
-0.2607
0.0292
-0.5652
-0.4075
0.0234
0.3214
0.1435
0.0743
0.3036
0.0387
0.2423
-29.0192
35.9897
-31.8002
8
3.2116
-3.3358
4.8593
22.1518
-8.8292
21.484
-0.1494
-0.8503
0.5523
0.9351
0.3792
0.4516
-0.0244
0.2268
-0.2299
0.4206
0.0884
0.004
0.4299
-0.1861
0.358
-20.4528
33.1895
-12.3019
9
3.8711
-3.5161
-3.9174
3.6563
2.2085
7.9627
-0.2509
-0.206
0.0156
0.108
0.2289
-0.0706
0.5187
0.105
0.022
0.1535
-0.0368
0.1111
0.1838
0.0756
0.415
-6.6843
11.7732
-37.4974
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
545 - 710
2
X-RAY DIFFRACTION
1
A
741 - 755
3
X-RAY DIFFRACTION
2
A
711 - 740
4
X-RAY DIFFRACTION
3
A
756 - 849
5
X-RAY DIFFRACTION
4
B
549 - 710
6
X-RAY DIFFRACTION
4
B
741 - 755
7
X-RAY DIFFRACTION
5
B
711 - 740
8
X-RAY DIFFRACTION
6
B
756 - 849
9
X-RAY DIFFRACTION
7
C
549 - 710
10
X-RAY DIFFRACTION
7
C
741 - 755
11
X-RAY DIFFRACTION
8
C
711 - 740
12
X-RAY DIFFRACTION
9
C
756 - 849
+
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