0.029958
0.017296
0.000000
0.000000
0.034593
0.000000
0.000000
0.000000
0.011406
0.00000
0.00000
0.00000
Hays, F.A.
Vargason, J.M.
Ho, P.S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
120.00
33.380
33.380
87.670
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
Na 1
22.990
SODIUM ION
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
147
N
NA
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
Biochemistry
BICHAW
0033
0006-2960
42
9586
9597
10.1021/bi0346603
12911300
Effect of Sequence on the Conformation of DNA Holliday Junctions
2003
10.2210/pdb1p4z/pdb
pdb_00001p4z
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
103.0
1
BENT CONICAL SI-MIRROR (RH COATING)
CCD
2002-07-18
ADSC QUANTUM 4
BENT GE(111) MONOCHROMATOR
SINGLE WAVELENGTH
M
x-ray
1
1.0
1.0
14-BM-C
APS
1.0
SYNCHROTRON
APS BEAMLINE 14-BM-C
3045.004
5'-D(*CP*CP*AP*GP*TP*AP*CP*TP*GP*G)-3'
1
syn
polymer
22.990
SODIUM ION
3
syn
non-polymer
18.015
water
64
nat
water
no
no
(DC)(DC)(DA)(DG)(DT)(DA)(DC)(DT)(DG)(DG)
CCAGTACTGG
A
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
1
1.87
33.78
7.50
0.6mM DNA, 5mM TRIS(HCl), 25mM Ca-Acetate, 7% MPD, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 7.50
293
TRIS(HCl)
1
Ca-Acetate
1
MPD
1
H2O
1
Ca-Acetate
2
MPD
2
TRIS(HCl)
2
H2O
2
-13.196
1
19
A
1
A
10
0.642
A_DC1:DG10_A
1
-2.093
-0.650
0.611
0.410
5.008
1
A
2
A
9
10.114
A_DC2:DG9_A
2
-8.075
-0.624
-0.315
0.424
-3.108
1
20
A
3
A
8
1.668
A_DA3:DT8_A
3
-19.925
-0.077
0.342
0.073
12.333
1
19
A
4
A
7
6.043
A_DG4:DC7_A
4
-18.762
-0.869
0.356
-0.147
-13.196
1
19
A
1
A
10
0.642
A_DC1:DG10_A
5
-2.093
-0.650
0.611
0.410
5.008
1
A
2
A
9
10.114
A_DC2:DG9_A
6
-8.075
-0.624
-0.315
0.424
-3.108
1
20
A
3
A
8
1.668
A_DA3:DT8_A
7
-19.925
-0.077
0.342
0.073
12.333
1
19
A
4
A
7
6.043
A_DG4:DC7_A
8
-18.762
-0.869
0.356
-0.147
2.697
27.097
A
A
1
2
5.417
A
A
10
9
2.750
2.470
0.392
0.197
AA_DC1DC2:DG9DG10_AA
1
10.499
-23.024
24.894
-0.122
1.473
3.516
51.867
A
A
2
3
5.007
A
A
9
8
3.324
4.375
-0.279
2.516
AA_DC2DA3:DT8DG9_AA
2
-1.108
1.268
51.684
2.569
0.241
3.036
27.255
A
A
3
4
8.376
A
A
8
7
3.195
3.916
0.731
0.249
AA_DA3DG4:DC7DT8_AA
3
-4.526
9.682
26.602
-0.416
-2.643
2.697
27.097
A
A
1
2
5.417
A
A
10
9
2.750
2.470
0.392
0.197
AA_DC1DC2:DG9DG10_AA
4
10.499
-23.024
24.894
-0.122
1.473
3.516
51.867
A
A
2
3
5.007
A
A
9
8
3.324
4.375
-0.279
2.516
AA_DC2DA3:DT8DG9_AA
5
-1.108
1.268
51.684
2.569
0.241
3.036
27.255
A
A
3
4
8.376
A
A
8
7
3.195
3.916
0.731
0.249
AA_DA3DG4:DC7DT8_AA
6
-4.526
9.682
26.602
-0.416
-2.643
chem_comp_atom
chem_comp_bond
database_2
struct_site
pdbx_initial_refinement_model
repository
Initial release
Version format compliance
Version format compliance
Atomic model
Data collection
Database references
Derived calculations
Refinement description
1
0
2003-09-02
1
1
2008-04-29
1
2
2011-07-13
1
3
2011-11-16
1
4
2024-02-14
1
5
2024-04-03
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Effect of Sequence on the Conformational Geometry of DNA Holliday Junctions
Effect of Sequence on the Conformational Geometry of DNA Holliday Junctions
RCSB
Y
RCSB
2003-04-24
REL
REL
NA
SODIUM ION
HOH
water
DNA was synthesized on an Applied Biosystems DNA synthesizer using phosphoramidite chemistry, with the trityl-protecting group left intact at the 5-terminal nucleotide, FOR SUBSEQUENT HPLC PURIFICATION, THEN DEPROTECTED BY TREATMENT WITH 3% ACETIC ACID FOR FIFTEEN MINUTES, NEUTRALIZED WITH AMMONIUM HYDROXIDE, AND DESALTED ON A SIGMA G-25 SEPHADEX COLUMN.
sample
UNPUBLISHED RESULTS OF STRUCTURE WITH ISOMORPHOUS UNIT CELL DIMENSIONS
Other
experimental model
NA
12
2
NA
NA
12
A
NA
13
2
NA
NA
13
A
NA
24
2
NA
NA
24
A
HOH
11
3
HOH
HOH
11
A
HOH
14
3
HOH
HOH
14
A
HOH
15
3
HOH
HOH
15
A
HOH
16
3
HOH
HOH
16
A
HOH
17
3
HOH
HOH
17
A
HOH
18
3
HOH
HOH
18
A
HOH
19
3
HOH
HOH
19
A
HOH
20
3
HOH
HOH
20
A
HOH
21
3
HOH
HOH
21
A
HOH
22
3
HOH
HOH
22
A
HOH
23
3
HOH
HOH
23
A
HOH
25
3
HOH
HOH
25
A
HOH
26
3
HOH
HOH
26
A
HOH
27
3
HOH
HOH
27
A
HOH
28
3
HOH
HOH
28
A
HOH
29
3
HOH
HOH
29
A
HOH
30
3
HOH
HOH
30
A
HOH
31
3
HOH
HOH
31
A
HOH
32
3
HOH
HOH
32
A
HOH
33
3
HOH
HOH
33
A
HOH
34
3
HOH
HOH
34
A
HOH
35
3
HOH
HOH
35
A
HOH
36
3
HOH
HOH
36
A
HOH
37
3
HOH
HOH
37
A
HOH
38
3
HOH
HOH
38
A
HOH
39
3
HOH
HOH
39
A
HOH
40
3
HOH
HOH
40
A
HOH
41
3
HOH
HOH
41
A
HOH
42
3
HOH
HOH
42
A
HOH
43
3
HOH
HOH
43
A
HOH
44
3
HOH
HOH
44
A
HOH
45
3
HOH
HOH
45
A
HOH
46
3
HOH
HOH
46
A
HOH
47
3
HOH
HOH
47
A
HOH
48
3
HOH
HOH
48
A
HOH
49
3
HOH
HOH
49
A
HOH
50
3
HOH
HOH
50
A
HOH
51
3
HOH
HOH
51
A
HOH
52
3
HOH
HOH
52
A
HOH
53
3
HOH
HOH
53
A
HOH
54
3
HOH
HOH
54
A
HOH
55
3
HOH
HOH
55
A
HOH
56
3
HOH
HOH
56
A
HOH
57
3
HOH
HOH
57
A
HOH
58
3
HOH
HOH
58
A
HOH
59
3
HOH
HOH
59
A
HOH
60
3
HOH
HOH
60
A
HOH
61
3
HOH
HOH
61
A
HOH
62
3
HOH
HOH
62
A
HOH
63
3
HOH
HOH
63
A
HOH
64
3
HOH
HOH
64
A
HOH
65
3
HOH
HOH
65
A
HOH
66
3
HOH
HOH
66
A
HOH
67
3
HOH
HOH
67
A
HOH
68
3
HOH
HOH
68
A
HOH
69
3
HOH
HOH
69
A
HOH
70
3
HOH
HOH
70
A
HOH
71
3
HOH
HOH
71
A
HOH
72
3
HOH
HOH
72
A
HOH
73
3
HOH
HOH
73
A
HOH
74
3
HOH
HOH
74
A
HOH
75
3
HOH
HOH
75
A
HOH
76
3
HOH
HOH
76
A
HOH
77
3
HOH
HOH
77
A
C
1
n
1
DC
1
A
C
2
n
2
DC
2
A
A
3
n
3
DA
3
A
G
4
n
4
DG
4
A
T
5
n
5
DT
5
A
A
6
n
6
DA
6
A
C
7
n
7
DC
7
A
T
8
n
8
DT
8
A
G
9
n
9
DG
9
A
G
10
n
10
DG
10
A
author_defined_assembly
2
dimeric
A
DC
2
A
OP2
DC
2
1_555
A
NA
12
B
NA
NA
1_555
A
HOH
25
E
O
HOH
1_555
127.0
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
0.5000000000
0.8660254038
0.0000000000
0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
12_545
x,x-y-1,-z+1/6
crystal symmetry operation
16.6900000000
-28.9079279783
14.6116666667
1
A
HOH
11
E
HOH
1
A
HOH
32
E
HOH
1
A
HOH
33
E
HOH
1
A
HOH
43
E
HOH
1
A
HOH
62
E
HOH
1
A
A
OP1
O
DT
HOH
8
16
2.04
1
A
DC
1
0.081
SIDE CHAIN
1
A
DG
9
0.095
SIDE CHAIN
1
A
A
O3'
C3'
DG
DG
10
10
-0.042
0.006
1.419
1.377
N
7.80
0.268
0.019
0.236
0.236
2.00
17.47
195
2143
2143
9.1
95.1
RANDOM
1
RESTRAINED
THROUGHOUT
0.000
MOLECULAR REPLACEMENT
UNPUBLISHED RESULTS OF STRUCTURE WITH ISOMORPHOUS UNIT CELL DIMENSIONS
0.33
0.26
5.00
0.23
0.24
2.00
17.47
64
269
3
202
0
0.015
1.7
18.30
2.23
0.251
0.055
0.242
2.13
21
244
6
7.9
74.6
3.6
2.000
17.470
1P4Z
2143
0.000
0.039
1
95.1
0.124
2.00
2.13
2.380
74.6
data reduction
DENZO
data scaling
SCALEPACK
phasing
EPMR
refinement
CNS
1.0
Effect of Sequence on the Conformational Geometry of DNA Holliday Junctions
1
N
N
2
N
N
2
N
N
2
N
N
3
N
N
THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ONE CHAIN. GENERATION OF THE DOUBLE HELIX CAN BE PERFORMED WITH THE FOLLOWING:
matrix=
(0.50000 0.86603 0.00000 )
(0.86603 -0.50000 0.00000 )
(0.00000 0.00000 -1.00000 )
translation=
(16.68855 -28.90537 14.61163)
metalc
2.825
A
DC
2
A
OP2
DC
2
1_555
A
NA
12
B
NA
NA
1_555
metalc
2.944
A
DG
4
A
OP2
DG
4
1_555
A
NA
13
C
NA
NA
1_555
metalc
2.713
A
NA
12
B
NA
NA
1_555
A
HOH
25
E
O
HOH
1_555
metalc
2.920
A
NA
24
D
NA
NA
1_555
A
HOH
42
E
O
HOH
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
A
DG
10
A
N1
DG
10
12_545
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
A
DG
10
A
O6
DG
10
12_545
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
A
DG
10
A
N2
DG
10
12_545
hydrog
DC-DG PAIR
A
DC
2
A
O2
DC
2
1_555
A
DG
9
A
N2
DG
9
12_545
hydrog
WATSON-CRICK
A
DA
3
A
N1
DA
3
1_555
A
DT
8
A
N3
DT
8
12_545
hydrog
WATSON-CRICK
A
DA
3
A
N6
DA
3
1_555
A
DT
8
A
O4
DT
8
12_545
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
A
DC
7
A
N3
DC
7
12_545
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
A
DC
7
A
O2
DC
7
12_545
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
A
DC
7
A
N4
DC
7
12_545
hydrog
WATSON-CRICK
A
DC
7
A
N3
DC
7
1_555
A
DG
4
A
N1
DG
4
12_545
hydrog
WATSON-CRICK
A
DC
7
A
N4
DC
7
1_555
A
DG
4
A
O6
DG
4
12_545
hydrog
WATSON-CRICK
A
DC
7
A
O2
DC
7
1_555
A
DG
4
A
N2
DG
4
12_545
hydrog
WATSON-CRICK
A
DT
8
A
N3
DT
8
1_555
A
DA
3
A
N1
DA
3
12_545
hydrog
WATSON-CRICK
A
DT
8
A
O4
DT
8
1_555
A
DA
3
A
N6
DA
3
12_545
hydrog
DG-DC PAIR
A
DG
9
A
N1
DG
9
1_555
A
DC
2
A
N3
DC
2
12_545
hydrog
WATSON-CRICK
A
DG
10
A
N1
DG
10
1_555
A
DC
1
A
N3
DC
1
12_545
hydrog
WATSON-CRICK
A
DG
10
A
N2
DG
10
1_555
A
DC
1
A
O2
DC
1
12_545
hydrog
WATSON-CRICK
A
DG
10
A
O6
DG
10
1_555
A
DC
1
A
N4
DC
1
12_545
DNA
B-DNA, Double Helix, DNA
1P4Z
PDB
1
1P4Z
1
10
1P4Z
1
10
1P4Z
A
1
1
10
BINDING SITE FOR RESIDUE NA A 12
A
NA
12
Software
2
BINDING SITE FOR RESIDUE NA A 13
A
NA
13
Software
1
BINDING SITE FOR RESIDUE NA A 24
A
NA
24
Software
2
A
DC
2
A
DC
2
2
1_555
A
HOH
25
E
HOH
2
1_555
A
DG
4
A
DG
4
1
1_555
A
DC
7
A
DC
7
2
1_555
A
HOH
42
E
HOH
2
1_555
178
P 61 2 2