1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Clore, G.M.
Kuszewski, J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
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
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
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
US
J.Am.Chem.Soc.
JACSAT
0004
0002-7863
123
3903
3918
10.1021/ja010033u
11457140
Improving the accuracy of NMR structures of DNA by means of a database potential of mean force describing base-base positional interactions.
2001
US
J.Am.Chem.Soc.
JACSAT
0004
0002-7863
122
6190
6200
10.1021/ja000324n
The NMR Structure of a DNA Dodecamer in an Aqueous Dilute Liquid Crystalline Phase
2000
10.2210/pdb1gip/pdb
pdb_00001gip
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
3663.392
5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
2
syn
polymer
no
no
(DC)(DG)(DC)(DG)(DA)(DA)(DT)(DT)(DC)(DG)(DC)(DG)
CGCGAATTCGCG
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
-1.425
1
19
A
1
B
24
0.224
A_DC1:DG24_B
1
-16.655
0.088
-0.059
-0.195
1.742
1
19
A
2
B
23
0.374
A_DG2:DC23_B
2
-11.590
-0.124
0.187
-0.172
-2.837
1
19
A
3
B
22
-1.866
A_DC3:DG22_B
3
-10.192
0.093
0.107
-0.164
3.882
1
19
A
4
B
21
-0.102
A_DG4:DC21_B
4
-10.441
-0.114
0.032
-0.178
0.519
1
20
A
5
B
20
2.414
A_DA5:DT20_B
5
-18.943
-0.027
-0.200
-0.125
1.840
1
20
A
6
B
19
2.064
A_DA6:DT19_B
6
-22.050
-0.021
-0.162
-0.136
-1.852
1
20
A
7
B
18
2.062
A_DT7:DA18_B
7
-22.052
0.022
-0.162
-0.136
-0.487
1
20
A
8
B
17
2.426
A_DT8:DA17_B
8
-18.942
0.028
-0.202
-0.126
-3.885
1
19
A
9
B
16
-0.090
A_DC9:DG16_B
9
-10.461
0.113
0.032
-0.178
2.809
1
19
A
10
B
15
-1.858
A_DG10:DC15_B
10
-10.169
-0.093
0.106
-0.164
-1.731
1
19
A
11
B
14
0.379
A_DC11:DG14_B
11
-11.575
0.125
0.185
-0.172
1.434
1
19
A
12
B
13
0.219
A_DG12:DC13_B
12
-16.675
-0.087
-0.061
-0.196
3.443
37.832
A
A
1
2
14.673
B
B
24
23
3.475
9.414
-0.281
0.244
AA_DC1DG2:DC23DG24_BB
1
-2.561
3.991
36.597
-0.927
0.079
3.609
33.693
A
A
2
3
-2.792
B
B
23
22
3.588
-1.618
-0.203
-0.622
AA_DG2DC3:DG22DC23_BB
2
0.621
-1.071
33.650
-0.784
0.461
3.396
34.808
A
A
3
4
17.699
B
B
22
21
3.435
10.435
-0.129
0.383
AA_DC3DG4:DC21DG22_BB
3
0.190
-0.322
33.253
-1.059
0.247
3.387
34.426
A
A
4
5
10.457
B
B
21
20
3.458
6.157
-0.147
-0.116
AA_DG4DA5:DT20DC21_BB
4
-0.359
0.609
33.886
-1.207
0.190
3.355
37.374
A
A
5
6
1.757
B
B
20
19
3.349
1.125
-0.231
0.008
AA_DA5DA6:DT19DT20_BB
5
-1.773
2.769
37.317
-0.139
0.120
3.381
37.005
A
A
6
7
-6.340
B
B
19
18
3.361
-4.016
-0.001
-0.363
AA_DA6DT7:DA18DT19_BB
6
-0.007
0.011
36.794
-0.014
0.000
3.354
37.371
A
A
7
8
1.745
B
B
18
17
3.348
1.117
0.231
0.009
AA_DT7DT8:DA17DA18_BB
7
1.788
-2.792
37.314
-0.137
-0.118
3.388
34.430
A
A
8
9
10.483
B
B
17
16
3.459
6.173
0.147
-0.116
AA_DT8DC9:DG16DA17_BB
8
0.346
-0.587
33.886
-1.210
-0.192
3.398
34.798
A
A
9
10
17.661
B
B
16
15
3.435
10.410
0.130
0.384
AA_DC9DG10:DC15DG16_BB
9
-0.190
0.322
33.250
-1.055
-0.248
3.608
33.701
A
A
10
11
-2.769
B
B
15
14
3.587
-1.605
0.203
-0.622
AA_DG10DC11:DG14DC15_BB
10
-0.609
1.051
33.658
-0.786
-0.459
3.442
37.831
A
A
11
12
14.697
B
B
14
13
3.475
9.429
0.281
0.243
AA_DC11DG12:DC13DG14_BB
11
2.564
-3.996
36.593
-0.929
-0.079
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Data collection
1
0
2001-08-01
1
1
2008-04-26
1
2
2011-07-13
1
3
2022-02-23
1
4
2023-12-27
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
DREW AND DICKERSON DODECAMER
HIGH RESOLUTION DREW AND DICKERSON DODECAMER
DODECAMER DETERMINED FROM DIPOLAR COUPLINGS
RCSB
Y
RCSB
2001-02-20
REL
THE NUMBER OF CALCULATED CONFORMERS IS 20 WITH NOES AND DIPOLAR COUPLINGS
AND 20 WITH DIPOLAR COUPLINGS ONLY
THE RESTRAINED REGULARIZED MEAN STRUCTURES
40
2
13C-HSQC-J-MODULATED
COSY
13C-HSQC-F1- COUPLED
15N-HSQC-F1- COUPLED
2D NOESY
40 mM
7.00
1
atm
308.00
K
THE STRUCTURE IS BASED ON A
TOTAL OF 162 NOE, 48 DISTANCES FOR WATSON-CRICK HYDROGEN BONDS, AND 137 DIHEDRAL
137 TORSION ANGLE RESTRAINTS, 198 CH AND 10 NH ONE-BOND DIPOLAR
COUPLING RESTRAINTS, AND 200 APPROXIMATE PROTON-PROTON
DIPOLAR COUPLINGS. THE EXPERIMENTAL RESTRAINTS ARE THE SAME AS THOSE
LISTED IN 1DUF. THE NON-BONDED CONTACTS ARE REPRESENTED
BY A QUARTIC VAN DER WAALS REPULSION TERM AND A BASE-BASE POSITIONING
DATABASE POTENTIAL OF MEAN FORCE. ALSO INCLUDED IS A TORSION ANGLE
DATABASE POTENTIAL OF MEAN FORCE.
IN THIS ENTRY THE SECOND TO LAST COLUMN REPRESENTS THE
AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SIMULATED
ANNEALING STRUCTURES AND THE MEAN COORDINATE POSITIONS.
MODEL 1 IS CALCULATED WITH NOE-DERIVED INTERPROTON
DISTANCE RESTRAINTS, DIPOLAR COUPLING
RESTRAINTS AND TORSION ANGLE RESTRAINTS.
MODEL 2 IS CALCULATED WITH DIPOLAR COUPLING AND TORSION
ANGLE RESTRAINTS. NO NOE-DERIVED INTERPROTON
DISTANCE RESTRAINTS WERE EMPLOYED.
STRUCTURAL STATISTICS:
----------------------------------------------------------
RESTRAINTS MODEL 1 MODEL 2
(# MODEL 1/# MODEL 2) (NOE + DIPOLARS) (DIPOLARS ONLY)
----------------------------------------------------------
RMS DEVIATIONS FROM EXPERIMENTAL RESTRAINTS
INTERPROTON DISTANCES (A) 0.065 0.114
(162/0)
TORSION ANGLES (DEG) 0 0
(137/137)
ALL DIPOLAR COUPLINGS (HZ) 2.8 2.6
(408/408)
RMS DEVIATIONS AND DIPOLAR COUPLING R-FACTORS
FOR DIFFERENT CLASSES OF DIPOLAR COUPLINGS
C-H RIBOSE (HZ/%) (94/94)* 2.27 (11.4%) 2.27 (11.4%)
C-H RIBOSE (HZ/%) (64/64)** 5.62 (28.1%) 5.24 (26.2%)
C-H BASE (HZ/%) (24/24)* 2.78 (13.9%) 2.81 (14.1%)
C-H BASE (HZ/%) (12/12)** 1.89 (9.26%) 2.01 (10.0%)
C-H METHYL (HZ/%) (4/4)* 0.98 (4.9%) 0.79 (4.0%)
N-H IMINO (HZ/%) (10/10)* 1.56 (15.9%) 1.50 (15.2%)
H-H ABSOLUTE VALUE (HZ)
(126/126) 1.26 1.25
H-H SIGN KNOWN (HZ) (74/74) 0.93 0.88
RMS DEVIATIONS FROM IDEALIZED COVALENT GEOMETRY
BONDS (A) 0.003 0.003
ANGLES (DEG) 0.897 0.925
IMPROPER TORSIONS (DEG) 0.296 0.106
----------------------------------------------------------
* MEASURED WITH AN ACCURACY OF +/- 2 HZ
** MEASURED WITH AN ACCURACY OF +/- 4 HZ
DIPOLAR COUPLING R-FACTOR = RATIO RMS DEVIATION BETWEEN
OBSERVED AND CALCULATED VALUES AND EXPECTED RMS DEVIATION
IF VECTORS ARE RANDOMLY DISTRIBUTED. THE LATTER IS GIVEN
BY {2DA**2[4 + 3H**2]/5}1/2 WHERE DA IS THE MAGNITUDE OF
THE AXIAL COMPONENT OF THE ALIGNMENT TENSOR AND H IS THE
RHOMBICITY. (ONLY APPLIES TO FIXED LENGTH VECTORS). THE
VALUES OF DA(CH), DA(NH) AND H ARE -16 HZ, -7.7 HZ AND
0.26, RESPECTIVELY.
SIMULATED ANNEALING IN TORSION ANGLE SPACE
USING A SIXTH ORDER PREDICTOR-CORRECTOR METHOD
WITH AUTOMATIC TIME STEP SELECTION
(C. SCHWIETERS AND G.M. CLORE)
0.5 MM DUPLEX DNA, 40MM SODIUM PHOSPHATE, PH 7.0
CLORE, SCHWIETERS AND KUSZEWSKI. ADAPTED FROM XPLOR 3.841 by BRUNGER ET AL.
refinement
NIH VERSION OF XPLOR (AVAILABLE TO ACADEMIC USERS BY ANONYMOUS FTP AT PORTAL.NIDDK.NIH.GOV IN pub/clore/xplor_nih)
structure solution
NMRPIPE 1.7
1999.039.11.31
structure solution
XwinNMR
2.4
structure solution
PIPP/CAPP
4.2.8
600
Bruker
DMX
750
Bruker
DMX
C
1
n
1
DC
1
A
G
2
n
2
DG
2
A
C
3
n
3
DC
3
A
G
4
n
4
DG
4
A
A
5
n
5
DA
5
A
A
6
n
6
DA
6
A
T
7
n
7
DT
7
A
T
8
n
8
DT
8
A
C
9
n
9
DC
9
A
G
10
n
10
DG
10
A
C
11
n
11
DC
11
A
G
12
n
12
DG
12
A
C
13
n
1
DC
13
B
G
14
n
2
DG
14
B
C
15
n
3
DC
15
B
G
16
n
4
DG
16
B
A
17
n
5
DA
17
B
A
18
n
6
DA
18
B
T
19
n
7
DT
19
B
T
20
n
8
DT
20
B
C
21
n
9
DC
21
B
G
22
n
10
DG
22
B
C
23
n
11
DC
23
B
G
24
n
12
DG
24
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
-3.65
0.60
122.90
119.25
A
A
A
C6
C5
C7
DT
DT
DT
8
8
8
N
1
-3.66
0.60
122.90
119.24
B
B
B
C6
C5
C7
DT
DT
DT
20
20
20
N
THE NMR STRUCTURE OF DNA DODECAMER DETERMINED IN AQUEOUS DILUTE LIQUID CRYSTALLINE PHASE
1
N
N
1
N
N
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
24
B
N1
DG
12
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
24
B
O6
DG
12
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
24
B
N2
DG
12
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
DC
23
B
N3
DC
11
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
DC
23
B
O2
DC
11
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
DC
23
B
N4
DC
11
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N3
DC
3
1_555
B
DG
22
B
N1
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N4
DC
3
1_555
B
DG
22
B
O6
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
3
A
O2
DC
3
1_555
B
DG
22
B
N2
DG
10
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
B
DC
21
B
N3
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
DC
21
B
O2
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
B
DC
21
B
N4
DC
9
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N1
DA
5
1_555
B
DT
20
B
N3
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N6
DA
5
1_555
B
DT
20
B
O4
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N1
DA
6
1_555
B
DT
19
B
N3
DT
7
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N6
DA
6
1_555
B
DT
19
B
O4
DT
7
1_555
hydrog
WATSON-CRICK
A
DT
7
A
N3
DT
7
1_555
B
DA
18
B
N1
DA
6
1_555
hydrog
WATSON-CRICK
A
DT
7
A
O4
DT
7
1_555
B
DA
18
B
N6
DA
6
1_555
hydrog
WATSON-CRICK
A
DT
8
A
N3
DT
8
1_555
B
DA
17
B
N1
DA
5
1_555
hydrog
WATSON-CRICK
A
DT
8
A
O4
DT
8
1_555
B
DA
17
B
N6
DA
5
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N3
DC
9
1_555
B
DG
16
B
N1
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N4
DC
9
1_555
B
DG
16
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
9
A
O2
DC
9
1_555
B
DG
16
B
N2
DG
4
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N1
DG
10
1_555
B
DC
15
B
N3
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N2
DG
10
1_555
B
DC
15
B
O2
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
10
A
O6
DG
10
1_555
B
DC
15
B
N4
DC
3
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N3
DC
11
1_555
B
DG
14
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N4
DC
11
1_555
B
DG
14
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
11
A
O2
DC
11
1_555
B
DG
14
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
A
DG
12
A
N1
DG
12
1_555
B
DC
13
B
N3
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
12
A
N2
DG
12
1_555
B
DC
13
B
O2
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
12
A
O6
DG
12
1_555
B
DC
13
B
N4
DC
1
1_555
DNA
B-DNA, DIPOLAR COUPLING, NOE, BASE-BASE ORIENTATIONAL POTENTIAL OF MEAN FORCE, DATABASE TORSION ANGLE POTENTIAL OF MEAN FORCE, DNA
1GIP
PDB
1
1GIP
1
12
1GIP
1
12
1GIP
A
1
1
12
13
24
1GIP
13
24
1GIP
B
1
1
12
1
P 1