0.007999
0.000000
0.000000
0.000000
0.007999
0.000000
0.000000
0.000000
0.037052
0.00000
0.00000
0.00000
Zhang, H.
Endrizzi, J.A.
Shu, Y.
Haque, F.
Sauter, C.
Guo, P.
Chi, Y.-I.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
125.012
125.012
26.989
C10 H14 N5 O7 P
347.221
y
ADENOSINE-5'-MONOPHOSPHATE
RNA linking
C9 H14 N3 O8 P
323.197
y
CYTIDINE-5'-MONOPHOSPHATE
RNA linking
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA linking
H2 O
18.015
WATER
non-polymer
Mn 2
54.938
MANGANESE (II) ION
non-polymer
C9 H13 N2 O9 P
324.181
y
URIDINE-5'-MONOPHOSPHATE
RNA linking
N
1
N
O
N
2
N
P
N
3
N
O
N
4
N
O
N
5
N
O
N
6
N
C
N
7
R
C
N
8
N
O
N
9
S
C
N
10
N
O
N
11
R
C
N
12
N
O
N
13
R
C
Y
14
N
N
Y
15
N
C
Y
16
N
N
Y
17
N
C
Y
18
N
C
N
19
N
N
Y
20
N
N
Y
21
N
C
Y
22
N
N
Y
23
N
C
N
24
N
H
N
25
N
H
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
O
N
39
N
P
N
40
N
O
N
41
N
O
N
42
N
O
N
43
N
C
N
44
R
C
N
45
N
O
N
46
S
C
N
47
N
O
N
48
R
C
N
49
N
O
N
50
R
C
N
51
N
N
N
52
N
C
N
53
N
O
N
54
N
N
N
55
N
C
N
56
N
N
N
57
N
C
N
58
N
C
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
N
64
N
H
N
65
N
H
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
O
N
74
N
P
N
75
N
O
N
76
N
O
N
77
N
O
N
78
N
C
N
79
R
C
N
80
N
O
N
81
S
C
N
82
N
O
N
83
R
C
N
84
N
O
N
85
R
C
Y
86
N
N
Y
87
N
C
Y
88
N
N
Y
89
N
C
N
90
N
C
N
91
N
O
N
92
N
N
N
93
N
C
N
94
N
N
N
95
N
N
Y
96
N
C
N
97
N
H
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
H
N
110
N
H
N
111
N
O
N
112
N
H
N
113
N
H
N
114
N
MN
N
115
N
O
N
116
N
P
N
117
N
O
N
118
N
O
N
119
N
O
N
120
N
C
N
121
R
C
N
122
N
O
N
123
S
C
N
124
N
O
N
125
R
C
N
126
N
O
N
127
R
C
N
128
N
N
N
129
N
C
N
130
N
O
N
131
N
N
N
132
N
C
N
133
N
O
N
134
N
C
N
135
N
C
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
H
N
145
N
H
N
146
N
H
N
147
N
H
N
148
N
H
N
1
N
sing
N
2
N
sing
N
3
N
doub
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
sing
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
Y
25
N
sing
Y
26
N
sing
Y
27
N
doub
N
28
N
sing
Y
29
N
sing
Y
30
N
sing
Y
31
N
doub
N
32
N
sing
Y
33
N
doub
N
34
N
sing
N
35
N
sing
Y
36
N
sing
Y
37
N
doub
N
38
N
sing
Y
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
doub
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
doub
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
doub
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
doub
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
Y
100
N
sing
Y
101
N
sing
Y
102
N
doub
N
103
N
sing
Y
104
N
sing
N
105
N
sing
Y
106
N
doub
N
107
N
doub
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
doub
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
doub
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
doub
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
doub
N
149
N
sing
N
150
N
doub
N
151
N
sing
N
152
N
sing
UK
Rna
RNARFU
2122
1355-8382
19
1226
1237
10.1261/rna.037077.112
23884902
Crystal structure of 3WJ core revealing divalent ion-promoted thermostability and assembly of the Phi29 hexameric motor pRNA.
2013
10.2210/pdb4kz2/pdb
pdb_00004kz2
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
CCD
2012-04-21
MARMOSAIC 225 mm CCD
Rosenbaum-Rock monochromator high-resolution double-crystal Si (111) sagittal focusing. Rosenbaum-Rock vertical focusing mirror.
SINGLE WAVELENGTH
M
x-ray
1
0.98789
1.0
22-BM
APS
0.98789
SYNCHROTRON
APS BEAMLINE 22-BM
5783.419
phi29 pRNA 3WJ core RNA 18 mer
1
syn
polymer
6241.711
phi29 pRNA 3WJ core RNA 20 mer
1
syn
polymer
5145.144
phi29 pRNA 3WJ core RNA 16 mer
1
syn
polymer
54.938
MANGANESE (II) ION
3
syn
non-polymer
18.015
water
2
nat
water
no
no
UUGCCAUGUGUAUGUGGG
UUGCCAUGUGUAUGUGGG
A
polyribonucleotide
no
no
CCCACAUACUUUGUUGAUCC
CCCACAUACUUUGUUGAUCC
B
polyribonucleotide
no
no
GGAUCAAUCAUGGCAA
GGAUCAAUCAUGGCAA
C
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
1
3.07
59.94
VAPOR DIFFUSION, HANGING DROP
4.6
100mM Sodium acetate, 24-26% MPD, 20mM CaCl2, 10mM MnCl2, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
295
-6.428
1
20
A
1
C
16
-1.786
A_U1:A16_C
1
-12.825
0.334
-0.132
-0.116
7.279
1
20
A
2
C
15
5.587
A_U2:A15_C
2
-5.535
0.079
0.272
-0.112
3.706
1
19
A
3
C
14
2.224
A_G3:C14_C
3
-3.703
-0.310
-0.279
-0.140
7.813
1
A
4
C
13
10.792
A_C4:G13_C
4
-5.692
-0.407
-0.124
0.283
7.795
1
A
5
C
12
10.957
A_C5:G12_C
5
-6.704
-0.443
-0.255
0.294
-4.873
1
20
A
6
C
11
6.278
A_A6:U11_C
6
-9.609
-0.191
-0.219
-0.048
-15.694
1
20
A
7
C
10
9.457
A_U7:A10_C
7
-13.972
-0.052
0.334
0.098
-3.066
1
19
A
8
C
9
8.151
A_G8:C9_C
8
-5.689
0.185
0.157
0.176
0.438
1
28
B
13
C
8
-0.503
B_G13:U8_C
9
-10.285
-2.662
0.035
-0.721
1.107
1
20
B
14
C
7
7.262
B_U14:A7_C
10
-11.495
0.278
0.057
-0.105
-3.752
1
20
B
15
C
6
5.021
B_U15:A6_C
11
-4.320
-0.117
0.130
-0.058
-8.793
1
19
B
16
C
5
2.816
B_G16:C5_C
12
-9.703
0.064
-0.299
-0.072
-3.231
1
20
B
17
C
4
-0.078
B_A17:U4_C
13
-12.109
0.128
-0.102
-0.039
4.892
1
20
B
18
C
3
1.032
B_U18:A3_C
14
-15.524
-0.280
0.002
-0.109
0.191
1
19
B
19
C
2
-0.980
B_C19:G2_C
15
-12.540
0.359
0.160
-0.207
2.102
1
19
B
20
C
1
4.181
B_C20:G1_C
16
-12.472
0.152
0.233
-0.064
-10.227
1
16
A
9
B
10
14.101
A_U9:U10_B
17
-9.872
-2.708
0.103
-1.782
-11.398
1
19
A
10
B
9
2.616
A_G10:C9_B
18
-11.451
-0.602
-0.230
-0.136
-5.228
1
20
A
11
B
8
2.663
A_U11:A8_B
19
-2.310
0.104
0.280
-0.036
-0.140
1
20
A
12
B
7
-2.650
A_A12:U7_B
20
-10.788
0.062
0.178
-0.024
4.909
A
13
B
6
9.144
A_U13:A6_B
21
-23.240
0.970
0.241
0.200
-9.027
1
19
A
14
B
5
3.906
A_G14:C5_B
22
-5.941
0.587
0.075
-0.089
-4.450
1
20
A
15
B
4
1.465
A_U15:A4_B
23
-4.629
-0.101
0.173
-0.105
-3.440
1
19
A
16
B
3
2.279
A_G16:C3_B
24
-7.492
0.144
-0.070
-0.151
-11.354
1
19
A
17
B
2
2.432
A_G17:C2_B
25
-11.251
0.017
-0.148
-0.137
-21.191
1
19
A
18
B
1
-0.729
A_G18:C1_B
26
-13.579
0.583
-0.229
-0.099
2.334
31.437
A
A
1
2
20.368
C
C
16
15
2.977
10.784
0.537
-1.085
AA_U1U2:A15A16_CC
1
-4.486
8.473
29.238
-3.706
-1.700
2.374
30.848
A
A
2
3
19.909
C
C
15
14
3.121
10.388
-0.266
-1.685
AA_U2G3:C14A15_CC
2
1.563
-2.996
29.045
-4.920
0.763
2.760
31.065
A
A
3
4
9.661
C
C
14
13
3.127
5.147
0.577
-1.694
AA_G3C4:G13C14_CC
3
-2.379
4.465
30.555
-4.059
-1.491
2.590
29.880
A
A
4
5
13.043
C
C
13
12
3.076
6.670
-0.217
-1.861
AA_C4C5:G12G13_CC
4
0.686
-1.341
29.134
-4.825
0.545
2.700
33.423
A
A
5
6
23.075
C
C
12
11
3.463
12.942
-0.133
-1.343
AA_C5A6:U11G12_CC
5
-0.449
0.801
30.879
-4.438
0.158
2.665
35.220
A
A
6
7
25.888
C
C
11
10
3.510
15.165
0.354
-1.150
AA_A6U7:A10U11_CC
6
-2.780
4.745
31.763
-4.148
-0.996
1.593
33.828
A
A
7
8
29.465
C
C
10
9
2.667
16.450
0.005
-1.579
AA_U7G8:C9A10_CC
7
-1.433
2.566
29.627
-4.567
-0.170
1.869
21.829
A
B
8
13
20.206
C
C
9
8
2.938
7.498
-0.015
-2.624
AB_G8G13:U8C9_CC
8
0.803
-2.163
20.500
-9.152
0.278
3.043
45.480
B
B
13
14
5.457
C
C
8
7
3.174
4.213
0.276
-1.255
BB_G13U14:A7U8_CC
9
-1.286
1.666
45.278
-1.977
-0.465
2.519
31.891
B
B
14
15
15.780
C
C
7
6
3.170
8.563
0.234
-2.095
BB_U14U15:A6A7_CC
10
2.073
-3.819
30.680
-5.195
-0.092
3.175
30.933
B
B
15
16
6.174
C
C
6
5
3.450
3.277
-0.341
-1.747
BB_U15G16:C5A6_CC
11
4.177
-7.869
30.485
-3.923
1.463
2.913
28.009
B
B
16
17
7.818
C
C
5
4
3.162
3.772
-0.239
-1.725
BB_G16A17:U4C5_CC
12
-0.948
1.965
27.743
-4.397
0.285
3.046
29.054
B
B
17
18
0.475
C
C
4
3
3.062
0.238
0.134
-1.729
BB_A17U18:A3U4_CC
13
-0.472
0.941
29.050
-3.495
-0.365
3.151
34.682
B
B
18
19
6.353
C
C
3
2
3.331
3.779
-0.219
-1.591
BB_U18C19:G2A3_CC
14
-1.653
2.780
34.443
-3.246
0.115
2.509
33.551
B
B
19
20
18.179
C
C
2
1
3.128
10.293
0.740
-1.836
BB_C19C20:G1G2_CC
15
5.087
-8.984
31.579
-4.684
-0.540
3.074
41.694
A
A
9
10
11.255
B
B
10
9
3.319
7.962
-0.561
-0.840
AA_U9G10:C9U10_BB
16
2.352
-3.325
40.895
-2.009
1.032
2.678
33.014
A
A
10
11
15.252
B
B
9
8
3.089
8.564
-0.039
-1.200
AA_G10U11:A8C9_BB
17
-2.693
4.797
31.802
-3.417
-0.343
2.523
31.263
A
A
11
12
16.241
B
B
8
7
2.985
8.634
0.229
-1.331
AA_U11A12:U7A8_BB
18
2.551
-4.799
29.970
-3.877
-0.009
2.619
40.781
A
A
12
13
18.379
B
B
7
6
3.084
12.610
0.941
-1.224
AA_A12U13:A6U7_BB
19
1.891
-2.757
38.818
-3.002
-1.164
2.788
31.932
A
A
13
14
16.724
B
B
6
5
3.325
9.080
-0.462
-1.485
AA_U13G14:C5A6_BB
20
-0.436
0.803
30.644
-4.273
0.765
2.893
28.233
A
A
14
15
7.970
B
B
5
4
3.133
3.875
-0.223
-1.612
AA_G14U15:A4C5_BB
21
-0.896
1.844
27.957
-4.139
0.264
2.807
32.669
A
A
15
16
14.319
B
B
4
3
3.169
7.974
0.185
-1.162
AA_U15G16:C3A4_BB
22
1.711
-3.072
31.662
-3.348
-0.053
2.809
30.560
A
A
16
17
13.659
B
B
3
2
3.365
7.133
0.512
-2.142
AA_G16G17:C2C3_BB
23
1.600
-3.065
29.693
-5.418
-0.668
3.331
36.046
A
A
17
18
5.829
B
B
2
1
3.527
3.587
0.297
-1.908
AA_G17G18:C1C2_BB
24
5.735
-9.320
35.427
-3.621
0.381
atom_site
atom_site_anisotrop
database_2
pdbx_struct_conn_angle
pdbx_unobs_or_zero_occ_atoms
struct_conn
struct_site
chem_comp_atom
chem_comp_bond
pdbx_initial_refinement_model
repository
Initial release
Advisory
Atomic model
Database references
Derived calculations
Data collection
Refinement description
1
0
2013-10-16
2
0
2022-06-08
2
1
2024-02-28
2
2
2024-04-03
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_asym_id
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr2_auth_asym_id
_pdbx_struct_conn_angle.ptnr2_label_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2013-05-29
REL
REL
MN
MANGANESE (II) ION
HOH
water
Chemically synthesized
sample
Chemically synthesized
sample
Chemically synthesized
sample
7 base pair A-form double helix
other
MN
2
4
MN
MN
101
A
MN
3
4
MN
MN
101
B
MN
1
4
MN
MN
101
C
HOH
4
5
HOH
HOH
201
A
HOH
5
5
HOH
HOH
202
A
U
1
n
1
U
1
A
U
2
n
2
U
2
A
G
3
n
3
G
3
A
C
4
n
4
C
4
A
C
5
n
5
C
5
A
A
6
n
6
A
6
A
U
7
n
7
U
7
A
G
8
n
8
G
8
A
U
9
n
9
U
9
A
G
10
n
10
G
10
A
U
11
n
11
U
11
A
A
12
n
12
A
12
A
U
13
n
13
U
13
A
G
14
n
14
G
14
A
U
15
n
15
U
15
A
G
16
n
16
G
16
A
G
17
n
17
G
17
A
G
18
n
18
G
18
A
C
1
n
1
C
1
B
C
2
n
2
C
2
B
C
3
n
3
C
3
B
A
4
n
4
A
4
B
C
5
n
5
C
5
B
A
6
n
6
A
6
B
U
7
n
7
U
7
B
A
8
n
8
A
8
B
C
9
n
9
C
9
B
U
10
n
10
U
10
B
U
11
n
11
U
11
B
U
12
n
12
U
12
B
G
13
n
13
G
13
B
U
14
n
14
U
14
B
U
15
n
15
U
15
B
G
16
n
16
G
16
B
A
17
n
17
A
17
B
U
18
n
18
U
18
B
C
19
n
19
C
19
B
C
20
n
20
C
20
B
G
1
n
1
G
1
C
G
2
n
2
G
2
C
A
3
n
3
A
3
C
U
4
n
4
U
4
C
C
5
n
5
C
5
C
A
6
n
6
A
6
C
A
7
n
7
A
7
C
U
8
n
8
U
8
C
C
9
n
9
C
9
C
A
10
n
10
A
10
C
U
11
n
11
U
11
C
G
12
n
12
G
12
C
G
13
n
13
G
13
C
C
14
n
14
C
14
C
A
15
n
15
A
15
C
A
16
n
16
A
16
C
author_and_software_defined_assembly
PISA
3
trimeric
3400
-28
9540
A
G
3
A
OP1
G
3
1_555
A
MN
101
D
MN
MN
1_555
C
A
7
C
OP1
A
7
1_555
164.9
A
C
4
A
OP1
C
4
1_555
C
MN
101
F
MN
MN
1_555
C
A
6
C
OP1
A
6
1_555
159.0
B
C
20
B
O3'
C
20
1_555
B
MN
101
E
MN
MN
1_555
B
C
20
B
O2'
C
20
1_555
71.0
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
1
A
OP2
U
2
A
OP2
U
2
1
Y
1
A
OP2
G
3
A
OP2
G
3
1
Y
1
A
OP2
C
4
A
OP2
C
4
1
Y
1
A
OP2
C
5
A
OP2
C
5
1
Y
1
A
OP2
A
6
A
OP2
A
6
1
Y
1
A
OP2
U
7
A
OP2
U
7
1
Y
1
A
OP2
G
8
A
OP2
G
8
1
Y
1
A
OP2
U
9
A
OP2
U
9
1
Y
1
A
OP2
G
10
A
OP2
G
10
1
Y
1
A
OP2
U
11
A
OP2
U
11
1
Y
1
A
OP2
A
12
A
OP2
A
12
1
Y
1
A
OP2
U
13
A
OP2
U
13
1
Y
1
A
OP2
G
14
A
OP2
G
14
1
Y
1
A
OP2
U
15
A
OP2
U
15
1
Y
1
A
OP2
G
16
A
OP2
G
16
1
Y
1
A
OP2
G
17
A
OP2
G
17
1
Y
1
A
OP2
G
18
A
OP2
G
18
1
Y
1
B
OP2
C
2
B
OP2
C
2
1
Y
1
B
OP2
C
3
B
OP2
C
3
1
Y
1
B
OP2
A
4
B
OP2
A
4
1
Y
1
B
OP2
C
5
B
OP2
C
5
1
Y
1
B
OP2
A
6
B
OP2
A
6
1
Y
1
B
OP2
U
7
B
OP2
U
7
1
Y
1
B
OP2
A
8
B
OP2
A
8
1
Y
1
B
OP2
C
9
B
OP2
C
9
1
Y
1
B
OP2
U
10
B
OP2
U
10
1
Y
1
B
OP2
U
11
B
OP2
U
11
1
Y
1
B
OP2
U
12
B
OP2
U
12
1
Y
1
B
OP2
G
13
B
OP2
G
13
1
Y
1
B
OP2
U
14
B
OP2
U
14
1
Y
1
B
OP2
U
15
B
OP2
U
15
1
Y
1
B
OP2
G
16
B
OP2
G
16
1
Y
1
B
OP2
A
17
B
OP2
A
17
1
Y
1
B
OP2
U
18
B
OP2
U
18
1
Y
1
B
OP2
C
19
B
OP2
C
19
1
Y
1
B
OP2
C
20
B
OP2
C
20
1
Y
1
C
OP2
G
2
C
OP2
G
2
1
Y
1
C
OP2
A
3
C
OP2
A
3
1
Y
1
C
OP2
U
4
C
OP2
U
4
1
Y
1
C
OP2
C
5
C
OP2
C
5
1
Y
1
C
OP2
A
6
C
OP2
A
6
1
Y
1
C
OP2
A
7
C
OP2
A
7
1
Y
1
C
OP2
U
8
C
OP2
U
8
1
Y
1
C
OP2
C
9
C
OP2
C
9
1
Y
1
C
OP2
A
10
C
OP2
A
10
1
Y
1
C
OP2
U
11
C
OP2
U
11
1
Y
1
C
OP2
G
12
C
OP2
G
12
1
Y
1
C
OP2
G
13
C
OP2
G
13
1
Y
1
C
OP2
C
14
C
OP2
C
14
1
Y
1
C
OP2
A
15
C
OP2
A
15
1
Y
1
C
OP2
A
16
C
OP2
A
16
1
Y
0.197
0.197
0.182
3.05
30.0
215
4203
4201
RANDOM
1
3
MOLECULAR REPLACEMENT
7 base-pair A-form helix
3.05
30.0
2
1139
3
1134
0
75.2
3.05
88.40
4KZ2
4217
4203
1.0
1.0
0.088
0.088
1
30.3
10.0
99.68
data collection
HKL-2000
model building
PHENIX
refinement
PHENIX
data reduction
HKL-2000
data scaling
HKL-2000
phasing
PHENIX
Crystal Structure of phi29 pRNA 3WJ Core
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
4
N
N
5
N
N
metalc
2.353
A
G
3
A
OP1
G
3
1_555
A
MN
101
D
MN
MN
1_555
metalc
2.334
A
C
4
A
OP1
C
4
1_555
C
MN
101
F
MN
MN
1_555
metalc
2.338
A
MN
101
D
MN
MN
1_555
C
A
7
C
OP1
A
7
1_555
metalc
2.042
B
C
20
B
O3'
C
20
1_555
B
MN
101
E
MN
MN
1_555
metalc
2.661
B
C
20
B
O2'
C
20
1_555
B
MN
101
E
MN
MN
1_555
metalc
2.165
C
A
6
C
OP1
A
6
1_555
C
MN
101
F
MN
MN
1_555
hydrog
WATSON-CRICK
A
U
1
A
N3
U
1
1_555
C
A
16
C
N1
A
16
1_555
hydrog
WATSON-CRICK
A
U
1
A
O4
U
1
1_555
C
A
16
C
N6
A
16
1_555
hydrog
WATSON-CRICK
A
U
2
A
N3
U
2
1_555
C
A
15
C
N1
A
15
1_555
hydrog
WATSON-CRICK
A
U
2
A
O4
U
2
1_555
C
A
15
C
N6
A
15
1_555
hydrog
WATSON-CRICK
A
G
3
A
N1
G
3
1_555
C
C
14
C
N3
C
14
1_555
hydrog
WATSON-CRICK
A
G
3
A
N2
G
3
1_555
C
C
14
C
O2
C
14
1_555
hydrog
WATSON-CRICK
A
G
3
A
O6
G
3
1_555
C
C
14
C
N4
C
14
1_555
hydrog
C-G PAIR
A
C
4
A
O2
C
4
1_555
C
G
13
C
N2
G
13
1_555
hydrog
C-G PAIR
A
C
5
A
O2
C
5
1_555
C
G
12
C
N2
G
12
1_555
hydrog
WATSON-CRICK
A
A
6
A
N1
A
6
1_555
C
U
11
C
N3
U
11
1_555
hydrog
WATSON-CRICK
A
A
6
A
N6
A
6
1_555
C
U
11
C
O4
U
11
1_555
hydrog
WATSON-CRICK
A
U
7
A
N3
U
7
1_555
C
A
10
C
N1
A
10
1_555
hydrog
WATSON-CRICK
A
U
7
A
O4
U
7
1_555
C
A
10
C
N6
A
10
1_555
hydrog
WATSON-CRICK
A
G
8
A
N1
G
8
1_555
C
C
9
C
N3
C
9
1_555
hydrog
WATSON-CRICK
A
G
8
A
N2
G
8
1_555
C
C
9
C
O2
C
9
1_555
hydrog
WATSON-CRICK
A
G
8
A
O6
G
8
1_555
C
C
9
C
N4
C
9
1_555
hydrog
TYPE_16_PAIR
A
U
9
A
N3
U
9
1_555
B
U
10
B
O2
U
10
1_555
hydrog
TYPE_16_PAIR
A
U
9
A
O4
U
9
1_555
B
U
10
B
N3
U
10
1_555
hydrog
WATSON-CRICK
A
G
10
A
N1
G
10
1_555
B
C
9
B
N3
C
9
1_555
hydrog
WATSON-CRICK
A
G
10
A
N2
G
10
1_555
B
C
9
B
O2
C
9
1_555
hydrog
WATSON-CRICK
A
G
10
A
O6
G
10
1_555
B
C
9
B
N4
C
9
1_555
hydrog
WATSON-CRICK
A
U
11
A
N3
U
11
1_555
B
A
8
B
N1
A
8
1_555
hydrog
WATSON-CRICK
A
U
11
A
O4
U
11
1_555
B
A
8
B
N6
A
8
1_555
hydrog
WATSON-CRICK
A
A
12
A
N1
A
12
1_555
B
U
7
B
N3
U
7
1_555
hydrog
WATSON-CRICK
A
A
12
A
N6
A
12
1_555
B
U
7
B
O4
U
7
1_555
hydrog
U-A PAIR
A
U
13
A
N3
U
13
1_555
B
A
6
B
N1
A
6
1_555
hydrog
WATSON-CRICK
A
G
14
A
N1
G
14
1_555
B
C
5
B
N3
C
5
1_555
hydrog
WATSON-CRICK
A
G
14
A
N2
G
14
1_555
B
C
5
B
O2
C
5
1_555
hydrog
WATSON-CRICK
A
G
14
A
O6
G
14
1_555
B
C
5
B
N4
C
5
1_555
hydrog
WATSON-CRICK
A
U
15
A
N3
U
15
1_555
B
A
4
B
N1
A
4
1_555
hydrog
WATSON-CRICK
A
U
15
A
O4
U
15
1_555
B
A
4
B
N6
A
4
1_555
hydrog
WATSON-CRICK
A
G
16
A
N1
G
16
1_555
B
C
3
B
N3
C
3
1_555
hydrog
WATSON-CRICK
A
G
16
A
N2
G
16
1_555
B
C
3
B
O2
C
3
1_555
hydrog
WATSON-CRICK
A
G
16
A
O6
G
16
1_555
B
C
3
B
N4
C
3
1_555
hydrog
WATSON-CRICK
A
G
17
A
N1
G
17
1_555
B
C
2
B
N3
C
2
1_555
hydrog
WATSON-CRICK
A
G
17
A
N2
G
17
1_555
B
C
2
B
O2
C
2
1_555
hydrog
WATSON-CRICK
A
G
17
A
O6
G
17
1_555
B
C
2
B
N4
C
2
1_555
hydrog
WATSON-CRICK
A
G
18
A
N1
G
18
1_555
B
C
1
B
N3
C
1
1_555
hydrog
WATSON-CRICK
A
G
18
A
N2
G
18
1_555
B
C
1
B
O2
C
1
1_555
hydrog
WATSON-CRICK
A
G
18
A
O6
G
18
1_555
B
C
1
B
N4
C
1
1_555
hydrog
TYPE_28_PAIR
B
G
13
B
N1
G
13
1_555
C
U
8
C
O2
U
8
1_555
hydrog
TYPE_28_PAIR
B
G
13
B
O6
G
13
1_555
C
U
8
C
N3
U
8
1_555
hydrog
WATSON-CRICK
B
U
14
B
N3
U
14
1_555
C
A
7
C
N1
A
7
1_555
hydrog
WATSON-CRICK
B
U
14
B
O4
U
14
1_555
C
A
7
C
N6
A
7
1_555
hydrog
WATSON-CRICK
B
U
15
B
N3
U
15
1_555
C
A
6
C
N1
A
6
1_555
hydrog
WATSON-CRICK
B
U
15
B
O4
U
15
1_555
C
A
6
C
N6
A
6
1_555
hydrog
WATSON-CRICK
B
G
16
B
N1
G
16
1_555
C
C
5
C
N3
C
5
1_555
hydrog
WATSON-CRICK
B
G
16
B
N2
G
16
1_555
C
C
5
C
O2
C
5
1_555
hydrog
WATSON-CRICK
B
G
16
B
O6
G
16
1_555
C
C
5
C
N4
C
5
1_555
hydrog
WATSON-CRICK
B
A
17
B
N1
A
17
1_555
C
U
4
C
N3
U
4
1_555
hydrog
WATSON-CRICK
B
A
17
B
N6
A
17
1_555
C
U
4
C
O4
U
4
1_555
hydrog
WATSON-CRICK
B
U
18
B
N3
U
18
1_555
C
A
3
C
N1
A
3
1_555
hydrog
WATSON-CRICK
B
U
18
B
O4
U
18
1_555
C
A
3
C
N6
A
3
1_555
hydrog
WATSON-CRICK
B
C
19
B
N3
C
19
1_555
C
G
2
C
N1
G
2
1_555
hydrog
WATSON-CRICK
B
C
19
B
N4
C
19
1_555
C
G
2
C
O6
G
2
1_555
hydrog
WATSON-CRICK
B
C
19
B
O2
C
19
1_555
C
G
2
C
N2
G
2
1_555
hydrog
WATSON-CRICK
B
C
20
B
N3
C
20
1_555
C
G
1
C
N1
G
1
1_555
hydrog
WATSON-CRICK
B
C
20
B
N4
C
20
1_555
C
G
1
C
O6
G
1
1_555
hydrog
WATSON-CRICK
B
C
20
B
O2
C
20
1_555
C
G
1
C
N2
G
1
1_555
RNA
phi29 DNA packaging motor pRNA core element, RNA
4KZ2
PDB
1
4KZ2
UUGCCAUGUGUAUGUGGG
4KZ2
PDB
2
4KZ2
CCCACAUACUUUGUUGAUCC
4KZ2
PDB
3
4KZ2
GGAUCAAUCAUGGCAA
1
18
4KZ2
1
18
4KZ2
A
1
1
18
1
20
4KZ2
1
20
4KZ2
B
2
1
20
1
16
4KZ2
1
16
4KZ2
C
3
1
16
BINDING SITE FOR RESIDUE MN A 101
A
MN
101
Software
3
BINDING SITE FOR RESIDUE MN B 101
B
MN
101
Software
1
BINDING SITE FOR RESIDUE MN C 101
C
MN
101
Software
4
A
G
3
A
G
3
3
1_555
B
C
19
B
C
19
3
6_554
C
A
7
C
A
7
3
1_555
B
C
20
B
C
20
1
1_555
A
C
4
A
C
4
4
1_555
A
G
18
A
G
18
4
3_655
B
C
20
B
C
20
4
6_554
C
A
6
C
A
6
4
1_555
79
I 4