0.015601
0.000000
0.009748
0.000000
0.038610
0.000000
0.000000
0.000000
0.029553
0.00000
0.00000
0.00000
Eichman, B.F.
Vargason, J.M.
Mooers, B.H.M.
Ho, P.S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
122.00
90.00
64.100
25.900
39.900
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O7 P
347.221
y
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
DNA linking
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
H2 O
18.015
WATER
non-polymer
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
N
C
N
12
R
C
Y
13
N
N
Y
14
N
C
Y
15
N
N
Y
16
N
C
Y
17
N
C
N
18
N
N
Y
19
N
N
Y
20
N
C
Y
21
N
N
Y
22
N
C
N
23
N
H
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
O
N
38
N
P
N
39
N
O
N
40
N
O
N
41
N
O
N
42
N
C
N
43
R
C
N
44
N
O
N
45
S
C
N
46
N
O
N
47
N
C
N
48
R
C
N
49
N
N
N
50
N
C
N
51
N
O
N
52
N
N
N
53
N
C
N
54
N
N
N
55
N
C
N
56
N
C
N
57
N
H
N
58
N
H
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
O
N
72
N
P
N
73
N
O
N
74
N
O
N
75
N
O
N
76
N
C
N
77
R
C
N
78
N
O
N
79
S
C
N
80
N
O
N
81
N
C
N
82
R
C
Y
83
N
N
Y
84
N
C
Y
85
N
N
Y
86
N
C
N
87
N
C
N
88
N
O
N
89
N
N
N
90
N
C
N
91
N
N
N
92
N
N
Y
93
N
C
N
94
N
H
N
95
N
H
N
96
N
H
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
O
N
109
N
P
N
110
N
O
N
111
N
O
N
112
N
O
N
113
N
C
N
114
R
C
N
115
N
O
N
116
S
C
N
117
N
O
N
118
N
C
N
119
R
C
N
120
N
N
N
121
N
C
N
122
N
O
N
123
N
N
N
124
N
C
N
125
N
O
N
126
N
C
N
127
N
C
N
128
N
C
N
129
N
H
N
130
N
H
N
131
N
H
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
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
O
N
145
N
H
N
146
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
Y
24
N
sing
Y
25
N
sing
Y
26
N
doub
N
27
N
sing
Y
28
N
sing
Y
29
N
sing
Y
30
N
doub
N
31
N
sing
Y
32
N
doub
N
33
N
sing
N
34
N
sing
Y
35
N
sing
Y
36
N
doub
N
37
N
sing
Y
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
doub
N
42
N
sing
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
doub
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
doub
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
doub
N
77
N
sing
N
78
N
sing
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
Y
97
N
sing
Y
98
N
sing
Y
99
N
doub
N
100
N
sing
Y
101
N
sing
N
102
N
sing
Y
103
N
doub
N
104
N
doub
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
doub
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
doub
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
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
doub
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
doub
N
143
N
sing
N
144
N
sing
N
145
N
doub
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
US
Proc.Natl.Acad.Sci.USA
PNASA6
0040
0027-8424
97
3971
3976
10.1073/pnas.97.8.3971
10760268
The Holliday junction in an inverted repeat DNA sequence: sequence effects on the structure of four-way junctions.
2000
10.2210/pdb1dcv/pdb
pdb_00001dcv
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
277.0
1
YALE MIRRORS
IMAGE PLATE
1999-06-15
RIGAKU RAXIS IV
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU RU300
3045.993
DNA (5'-D(*CP*CP*GP*CP*TP*AP*GP*CP*GP*G)-3')
2
syn
polymer
18.015
water
23
nat
water
no
no
(DC)(DC)(DG)(DC)(DT)(DA)(DG)(DC)(DG)(DG)
CCGCTAGCGG
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
1
2.20
44.12
7.00
pH 7.00
-7.012
1
19
A
1
B
20
2.071
A_DC1:DG20_B
1
-17.384
0.053
0.037
-0.172
3.846
1
19
A
2
B
19
3.961
A_DC2:DG19_B
2
-5.500
-0.635
0.065
0.032
-6.708
1
19
A
3
B
18
5.436
A_DG3:DC18_B
3
-19.335
0.093
0.278
0.201
-6.419
1
19
A
4
B
17
2.888
A_DC4:DG17_B
4
-1.514
-0.371
0.169
-0.127
-3.744
1
20
A
5
B
16
0.917
A_DT5:DA16_B
5
-7.751
-0.423
-0.008
-0.272
3.264
1
20
A
6
B
15
-9.355
A_DA6:DT15_B
6
-15.421
0.215
0.429
-0.082
4.168
1
19
A
7
B
14
-2.837
A_DG7:DC14_B
7
0.962
0.526
0.279
-0.128
-4.219
1
19
A
8
B
13
-10.051
A_DC8:DG13_B
8
-8.935
1.120
0.166
-0.473
-8.515
1
19
A
9
B
12
0.241
A_DG9:DC12_B
9
-9.615
0.891
-0.299
0.150
10.382
1
19
A
10
B
11
-8.787
A_DG10:DC11_B
10
-3.096
0.334
0.802
-0.316
3.160
38.271
A
A
1
2
-1.494
B
B
20
19
3.212
-0.979
0.331
2.174
AA_DC1DC2:DG19DG20_BB
1
0.307
-0.468
38.258
3.435
-0.467
3.917
41.706
A
A
2
3
6.079
B
B
19
18
3.734
4.317
-0.494
1.767
AA_DC2DG3:DC18DG19_BB
2
-3.328
4.686
41.364
1.948
0.282
3.436
32.001
A
A
3
4
-5.339
B
B
18
17
3.394
-2.939
0.040
-0.628
AA_DG3DC4:DG17DC18_BB
3
-0.281
0.510
31.868
-0.584
-0.126
3.422
26.962
A
A
4
5
5.104
B
B
17
16
3.458
2.372
-0.269
0.303
AA_DC4DT5:DA16DG17_BB
4
2.959
-6.368
26.699
0.010
1.377
3.027
48.795
A
A
5
6
-5.692
B
B
16
15
3.177
-4.694
-0.267
1.618
AA_DT5DA6:DT15DA16_BB
5
-2.461
2.984
48.524
2.299
0.145
3.446
38.294
A
A
6
7
4.866
B
B
15
14
3.450
3.187
0.447
-0.163
AA_DA6DG7:DC14DT15_BB
6
2.296
-3.506
38.099
-0.670
-0.377
3.603
35.438
A
A
7
8
-1.702
B
B
14
13
3.622
-1.035
-0.418
-0.145
AA_DG7DC8:DG13DC14_BB
7
1.558
-2.560
35.391
-0.070
0.939
3.711
36.833
A
A
8
9
8.693
B
B
13
12
3.643
5.458
0.639
0.375
AA_DC8DG9:DC12DG13_BB
8
4.996
-7.957
36.108
-0.248
-0.241
2.723
36.751
A
A
9
10
-5.399
B
B
12
11
2.961
-3.338
-0.124
1.189
AA_DG9DG10:DC11DC12_BB
9
-12.324
19.934
34.534
2.295
-1.313
software
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
repository
Initial release
Version format compliance
Version format compliance
Refinement description
Data collection
Database references
Refinement description
1
0
2000-04-17
1
1
2008-04-27
1
2
2011-07-13
1
3
2017-10-04
1
4
2024-02-07
1
5
2024-04-03
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
RCSB
Y
RCSB
1999-11-05
REL
REL
HOH
water
IDEAL B-DNA
Other
in silico model
HOH
23
2
HOH
HOH
23
A
HOH
24
2
HOH
HOH
24
A
HOH
25
2
HOH
HOH
25
A
HOH
27
2
HOH
HOH
27
A
HOH
28
2
HOH
HOH
28
A
HOH
30
2
HOH
HOH
30
A
HOH
32
2
HOH
HOH
32
A
HOH
35
2
HOH
HOH
35
A
HOH
37
2
HOH
HOH
37
A
HOH
38
2
HOH
HOH
38
A
HOH
40
2
HOH
HOH
40
A
HOH
41
2
HOH
HOH
41
A
HOH
42
2
HOH
HOH
42
A
HOH
21
2
HOH
HOH
21
B
HOH
22
2
HOH
HOH
22
B
HOH
26
2
HOH
HOH
26
B
HOH
29
2
HOH
HOH
29
B
HOH
31
2
HOH
HOH
31
B
HOH
33
2
HOH
HOH
33
B
HOH
34
2
HOH
HOH
34
B
HOH
36
2
HOH
HOH
36
B
HOH
39
2
HOH
HOH
39
B
HOH
43
2
HOH
HOH
43
B
C
1
n
1
DC
1
A
C
2
n
2
DC
2
A
G
3
n
3
DG
3
A
C
4
n
4
DC
4
A
T
5
n
5
DT
5
A
A
6
n
6
DA
6
A
G
7
n
7
DG
7
A
C
8
n
8
DC
8
A
G
9
n
9
DG
9
A
G
10
n
10
DG
10
A
C
11
n
1
DC
11
B
C
12
n
2
DC
12
B
G
13
n
3
DG
13
B
C
14
n
4
DC
14
B
T
15
n
5
DT
15
B
A
16
n
6
DA
16
B
G
17
n
7
DG
17
B
C
18
n
8
DC
18
B
G
19
n
9
DG
19
B
G
20
n
10
DG
20
B
author_defined_assembly
2
dimeric
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
A
O4'
O
DC
HOH
8
42
2.18
-8.58410
0.00000
-1.84650
16.88670
0.00000
-8.30250
ANISOTROPIC B VALUES WERE APPLIED TO FCALC DURING REFINEMENT IN ORDER TO SCALE FCALC TO FOBS
0.3170000
0.2070000
0.2070000
2.50
10.00
178
1943
10.000
98.6
RANDOM
1
THROUGHOUT
2.000
MOLECULAR REPLACEMENT
IDEAL B-DNA
2.50
10.00
23
427
0
404
0
0.005
1.00
2.59
22
144
10
95.4
21.60
2.490
33.810
1DCV
2009
0.000
0.0500000
1
12.8000
3.700
98.2
0.4180000
2.49
2.58
3.1
3.37
91.6
phasing
EPMR
refinement
X-PLOR
3.851
data scaling
d*TREK
B-DNA DECAMER WITH CENTRAL TA DINUCLEOTIDE
1
N
N
1
N
N
2
N
N
2
N
N
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
20
B
N1
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
20
B
O6
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
20
B
N2
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N3
DC
2
1_555
B
DG
19
B
N1
DG
9
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
B
DG
19
B
O6
DG
9
1_555
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
B
DG
19
B
N2
DG
9
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N1
DG
3
1_555
B
DC
18
B
N3
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N2
DG
3
1_555
B
DC
18
B
O2
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
3
A
O6
DG
3
1_555
B
DC
18
B
N4
DC
8
1_555
hydrog
WATSON-CRICK
A
DC
4
A
N3
DC
4
1_555
B
DG
17
B
N1
DG
7
1_555
hydrog
WATSON-CRICK
A
DC
4
A
N4
DC
4
1_555
B
DG
17
B
O6
DG
7
1_555
hydrog
WATSON-CRICK
A
DC
4
A
O2
DC
4
1_555
B
DG
17
B
N2
DG
7
1_555
hydrog
WATSON-CRICK
A
DT
5
A
N3
DT
5
1_555
B
DA
16
B
N1
DA
6
1_555
hydrog
WATSON-CRICK
A
DT
5
A
O4
DT
5
1_555
B
DA
16
B
N6
DA
6
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N1
DA
6
1_555
B
DT
15
B
N3
DT
5
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N6
DA
6
1_555
B
DT
15
B
O4
DT
5
1_555
hydrog
WATSON-CRICK
A
DG
7
A
N1
DG
7
1_555
B
DC
14
B
N3
DC
4
1_555
hydrog
WATSON-CRICK
A
DG
7
A
N2
DG
7
1_555
B
DC
14
B
O2
DC
4
1_555
hydrog
WATSON-CRICK
A
DG
7
A
O6
DG
7
1_555
B
DC
14
B
N4
DC
4
1_555
hydrog
WATSON-CRICK
A
DC
8
A
N3
DC
8
1_555
B
DG
13
B
N1
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
8
A
N4
DC
8
1_555
B
DG
13
B
O6
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
8
A
O2
DC
8
1_555
B
DG
13
B
N2
DG
3
1_555
hydrog
WATSON-CRICK
A
DG
9
A
N1
DG
9
1_555
B
DC
12
B
N3
DC
2
1_555
hydrog
WATSON-CRICK
A
DG
9
A
N2
DG
9
1_555
B
DC
12
B
O2
DC
2
1_555
hydrog
WATSON-CRICK
A
DG
9
A
O6
DG
9
1_555
B
DC
12
B
N4
DC
2
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N1
DG
10
1_555
B
DC
11
B
N3
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N2
DG
10
1_555
B
DC
11
B
O2
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
10
A
O6
DG
10
1_555
B
DC
11
B
N4
DC
1
1_555
DNA
CENTRAL TA DINUCLEOTIDE, DEOXYRIBONUCLEIC ACID, DNA
1DCV
PDB
1
1DCV
1
10
1DCV
1
10
1DCV
A
1
1
10
11
20
1DCV
11
20
1DCV
B
1
1
10
5
monoclinic
C 1 2 1