0.013867
0.000000
0.005783
0.000000
0.042282
0.000000
0.000000
0.000000
0.029946
0.00000
0.00000
0.00000
Eichman, B.F.
Mooers, B.H.M.
Alberti, M.
Hearst, J.E.
Ho, P.S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
112.64
90.00
72.116
23.651
36.182
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
C15 H14 O4
258.269
4'-HYDROXYMETHYL-4,5',8-TRIMETHYLPSORALEN
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
Y
147
N
O
Y
148
N
C
Y
149
N
C
Y
150
N
C
Y
151
N
C
Y
152
N
C
Y
153
N
C
Y
154
N
C
Y
155
N
C
Y
156
N
C
Y
157
N
C
Y
158
N
C
Y
159
N
O
N
160
N
O
N
161
N
C
N
162
N
C
N
163
N
O
N
164
N
C
N
165
N
C
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
H
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
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
Y
152
N
sing
Y
153
N
sing
Y
154
N
sing
N
155
N
doub
Y
156
N
doub
N
157
N
sing
Y
158
N
sing
N
159
N
sing
Y
160
N
doub
Y
161
N
sing
N
162
N
sing
Y
163
N
sing
Y
164
N
sing
Y
165
N
doub
Y
166
N
sing
Y
167
N
sing
N
168
N
sing
Y
169
N
doub
Y
170
N
doub
N
171
N
sing
Y
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
308
15
26
10.1006/jmbi.2001.4567
11302703
The crystal structures of psoralen cross-linked DNAs: drug-dependent formation of Holliday junctions.
2001
US
Proc.Natl.Acad.Sci.USA
PNASA6
0040
0027-8424
97
3971
3976
10.1073/pnas.97.8.3971
The Holliday junction in an inverted repeat DNA sequence: Sequence effects on the structure of four-way junctions
2000
10.2210/pdb1fhz/pdb
pdb_00001fhz
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
298.0
1
CCD
1999-10-08
ADSC QUANTUM 4
SINGLE WAVELENGTH
M
x-ray
1
1.100
1.0
5.0.2
ALS
1.100
SYNCHROTRON
ALS BEAMLINE 5.0.2
DNA IS CROSS-LINKED BY PSORALEN
3045.992
DNA (5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3')
2
syn
polymer
258.269
4'-HYDROXYMETHYL-4,5',8-TRIMETHYLPSORALEN
1
syn
non-polymer
18.015
water
43
nat
water
no
no
(DC)(DC)(DG)(DG)(DT)(DA)(DC)(DC)(DG)(DG)
CCGGTACCGG
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
1
2.23
44.89
VAPOR DIFFUSION, SITTING DROP
7
sodium cacodylate, MgCl2, MPD, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 277K
277
sodium cacodylate
1
MgCl2
1
MPD
1
MgCl2
2
MPD
2
-45.332
1
20
A
6
B
15
13.809
A_DA6:DT15_B
1
-16.125
-0.348
-0.898
0.310
-4.755
1
19
A
7
B
14
-0.696
A_DC7:DG14_B
2
-2.384
0.089
0.181
-0.083
10.732
1
19
A
8
B
13
4.540
A_DC8:DG13_B
3
-6.969
0.554
-0.175
-0.080
8.416
1
19
A
9
B
12
1.511
A_DG9:DC12_B
4
-6.914
-0.183
0.253
0.014
2.192
1
19
A
10
B
11
1.475
A_DG10:DC11_B
5
-17.746
-0.285
0.030
-0.158
2.543
25.594
A
A
6
7
9.166
B
B
15
14
2.386
3.799
-0.811
1.029
AA_DA6DC7:DG14DT15_BB
1
-14.754
35.600
20.626
1.419
-1.678
2.943
41.353
A
A
7
8
-0.021
B
B
14
13
2.960
-0.015
0.165
2.171
AA_DC7DC8:DG13DG14_BB
2
7.506
-10.684
40.696
3.076
0.498
3.352
37.626
A
A
8
9
-1.057
B
B
13
12
3.407
-0.682
0.180
3.080
AA_DC8DG9:DC12DG13_BB
3
-0.164
0.254
37.620
4.867
-0.301
3.911
42.529
A
A
9
10
5.382
B
B
12
11
3.689
3.894
-0.180
2.681
AA_DG9DG10:DC11DC12_BB
4
-3.627
5.013
42.210
3.236
-0.180
chem_comp_atom
chem_comp_bond
database_2
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2001-04-21
1
1
2008-04-27
1
2
2011-07-13
1
3
2024-02-07
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
native d(CCGGTACCGG)
NDB
Y
NDB
2000-08-02
REL
REL
PSO
4'-HYDROXYMETHYL-4,5',8-TRIMETHYLPSORALEN
HOH
water
PSO
21
2
PSO
PSO
21
B
HOH
22
3
HOH
HOH
22
A
HOH
23
3
HOH
HOH
23
A
HOH
24
3
HOH
HOH
24
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
33
3
HOH
HOH
33
A
HOH
34
3
HOH
HOH
34
A
HOH
38
3
HOH
HOH
38
A
HOH
40
3
HOH
HOH
40
A
HOH
41
3
HOH
HOH
41
A
HOH
42
3
HOH
HOH
42
A
HOH
46
3
HOH
HOH
46
A
HOH
47
3
HOH
HOH
47
A
HOH
48
3
HOH
HOH
48
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
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
25
3
HOH
HOH
25
B
HOH
26
3
HOH
HOH
26
B
HOH
32
3
HOH
HOH
32
B
HOH
35
3
HOH
HOH
35
B
HOH
36
3
HOH
HOH
36
B
HOH
37
3
HOH
HOH
37
B
HOH
39
3
HOH
HOH
39
B
HOH
43
3
HOH
HOH
43
B
HOH
44
3
HOH
HOH
44
B
HOH
45
3
HOH
HOH
45
B
HOH
49
3
HOH
HOH
49
B
HOH
50
3
HOH
HOH
50
B
HOH
55
3
HOH
HOH
55
B
HOH
56
3
HOH
HOH
56
B
HOH
57
3
HOH
HOH
57
B
HOH
58
3
HOH
HOH
58
B
HOH
59
3
HOH
HOH
59
B
HOH
60
3
HOH
HOH
60
B
C
1
n
1
DC
1
A
C
2
n
2
DC
2
A
G
3
n
3
DG
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
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
G
14
n
4
DG
14
B
T
15
n
5
DT
15
B
A
16
n
6
DA
16
B
C
17
n
7
DC
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
4
tetrameric
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
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
2_655
-x+1,y,-z
crystal symmetry operation
72.1160000000
0.0000000000
0.0000000000
1
A
HOH
62
D
HOH
1
A
B
C6
C4
DT
PSO
5
21
2.10
1
B
B
C5
C5'
DT
PSO
15
21
2.16
1
B
DT
15
0.084
SIDE CHAIN
1
-5.85
0.60
123.70
117.85
A
A
A
C5
C6
N1
DT
DT
DT
5
5
5
N
1
-11.18
0.60
119.00
107.82
A
A
A
C4
C5
C7
DT
DT
DT
5
5
5
N
1
-15.32
0.60
122.90
107.58
A
A
A
C6
C5
C7
DT
DT
DT
5
5
5
N
1
-5.98
0.60
123.70
117.72
B
B
B
C5
C6
N1
DT
DT
DT
15
15
15
N
1
-10.92
0.60
119.00
108.08
B
B
B
C4
C5
C7
DT
DT
DT
15
15
15
N
1
-15.05
0.60
122.90
107.85
B
B
B
C6
C5
C7
DT
DT
DT
15
15
15
N
1
A
A
C4
C5
DT
DT
5
5
0.056
0.009
1.445
1.501
N
1
A
A
C5
C6
DT
DT
5
5
0.199
0.007
1.339
1.538
N
1
A
A
C6
N1
DT
DT
5
5
0.063
0.007
1.378
1.441
N
1
B
B
C4
C5
DT
DT
15
15
0.054
0.009
1.445
1.499
N
1
B
B
C5
C6
DT
DT
15
15
0.199
0.007
1.339
1.538
N
1
B
B
C6
N1
DT
DT
15
15
0.073
0.007
1.378
1.451
N
-8.0249
0.0000
-0.0139
13.3859
0.0000
-5.3610
ANISOTROPIC B VALUES WERE APPLIED TO FCALC DURING REFINEMENT IN
ORDER TO SCALE FCALC TO FOBS
0.311
0.228
0.236
0.236
2.20
33.39
305
2891
2891
10.5
96.5
random
1
THROUGHOUT
0.0
MOLECULAR REPLACEMENT
Parkinson et al.
2.20
33.39
43
466
19
404
0
0.015
1.594
2.20
33.39
1FHZ
2900
2900
-3
0.067
1
12.3
3.3
96.7
0.1
2.20
2.28
284
3.3
98.3
data reduction
DENZO
data scaling
SCALEPACK
model building
X-PLOR
refinement
X-PLOR
3.851
phasing
X-PLOR
PSORALEN CROSS-LINKED D(CCGGTACCGG) FORMS HOLLIDAY JUNCTION
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
A four-way junction is a dimer constructed from chains A and B and a
symmetry partner generated by the two-fold
covale
1.559
none
A
DT
5
A
C5
DT
5
1_555
B
PSO
21
C
C4
PSO
1_555
covale
1.560
none
A
DT
5
A
C6
DT
5
1_555
B
PSO
21
C
C3
PSO
1_555
covale
1.553
none
B
DT
15
B
C5
DT
5
1_555
B
PSO
21
C
C4'
PSO
1_555
covale
1.566
none
B
DT
15
B
C6
DT
5
1_555
B
PSO
21
C
C5'
PSO
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
DC
7
A
N3
DC
7
1_555
B
DG
14
B
N1
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
7
A
N4
DC
7
1_555
B
DG
14
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
7
A
O2
DC
7
1_555
B
DG
14
B
N2
DG
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
psoralen, cross-linked DNA, Holliday junction, DNA-drug complex, DNA
1FHZ
PDB
1
1FHZ
1
10
1FHZ
1
10
1FHZ
A
1
1
10
11
20
1FHZ
11
20
1FHZ
B
1
1
10
BINDING SITE FOR RESIDUE PSO B 21
B
PSO
21
Software
4
A
DT
5
A
DT
5
4
1_555
A
DA
6
A
DA
6
4
1_555
B
DT
15
B
DT
5
4
1_555
B
DA
16
B
DA
6
4
1_555
5
monoclinic
C 1 2 1