1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Padrta, P.
Stefl, R.
Zidek, L.
Sklenar, V.
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
NE
J.Biomol.NMR
JBNME9
0800
0925-2738
24
1
14
10.1023/A:1020632900961
12449414
Refinement of d(GCGAAGC) Hairpin Structure Using One- and Two-Bond Residual Dipolar Couplings
2002
10.2210/pdb1pqt/pdb
pdb_00001pqt
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
1
1.0
2147.437
5'-D(*GP*CP*GP*AP*AP*GP*C)-3'
1
syn
polymer
no
no
(DG)(DC)(DG)(DA)(DA)(DG)(DC)
GCGAAGC
A
polydeoxyribonucleotide
n
n
n
n
n
n
n
-3.693
1
19
A
1
A
7
-0.092
A_DG1:DC7_A
1
5.939
-0.440
0.077
-0.215
16.068
1
19
A
2
A
6
-0.416
A_DC2:DG6_A
2
12.675
0.178
-0.255
-0.149
32.817
9
11
A
3
A
5
15.015
A_DG3:DA5_A
3
-2.319
6.211
1.254
-4.034
2.883
32.539
A
A
1
2
10.410
A
A
7
6
2.921
5.802
0.781
-0.126
AA_DG1DC2:DG6DC7_AA
1
1.326
-2.379
32.005
-1.132
-1.187
3.048
48.694
A
A
2
3
13.079
A
A
6
5
2.824
10.706
-0.106
1.380
AA_DC2DG3:DA5DG6_AA
2
0.319
-0.390
47.572
0.929
0.151
database_2
pdbx_nmr_software
pdbx_nmr_spectrometer
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2003-07-01
1
1
2008-04-29
1
2
2011-07-13
1
3
2022-03-02
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_pdbx_nmr_spectrometer.model
1KR8 is the same DNA hairpin but calculated with the simple parabolic potential as the penalty function for RDC restraints, unlike this entry where the flat-bottom potential was used for RDCs instead.
RCSB
Y
RCSB
2003-06-19
REL
REL
THIS SEQUENCE OCCURS NATURALLY IN REPLICATION ORIGINS OF PHAGE PHIX174, IN HERPES SIMPLEX VIRUS, IN E. COLI HEAT-SHOCK GENE AND RRNA GENES.
sample
THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY IN ISOTROPIC AND LIQUID CRYSTALLINE PHASE.
all calculated structures submitted
14
14
2D NOESY
E-COSY
DQF-COSY
COUPLED HSQC
S3E E-COSY
10 mM
6.7
1
atm
303
K
molecular dynamics
7
6MM NATURAL ABUNDANCE D(GCGAAGC), 10MM PHOSPHATE BUFFER NA, D2O; 6MM NATURAL ABUNDANCE D(GCGAAGC), 10MM PHOSPHATE BUFFER NA, 90% H2O, 10% D2O; U-15N,13C, 0.5MM D(GCGAAGC), 10MM PHOSPHATE BUFFER NA, 90% H2O, 10% D2O
KOLLMAN, CASE ET. AL
refinement
Amber
7.0
Bruker
collection
XwinNMR
2.1
Bruker
collection
XwinNMR
3.0
T. D. Goddard and D. G. Kneller
data analysis
Sparky
3.X
KOLLMAN, CASE ET. AL
structure solution
Amber
7.0
500
Bruker
AVANCE
G
1
n
1
DG
1
A
C
2
n
2
DC
2
A
G
3
n
3
DG
3
A
A
4
n
4
DA
4
A
A
5
n
5
DA
5
A
G
6
n
6
DG
6
A
C
7
n
7
DC
7
A
author_defined_assembly
1
monomeric
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
DA
4
0.085
SIDE CHAIN
1
A
DA
5
0.057
SIDE CHAIN
1
A
DG
6
0.065
SIDE CHAIN
2
A
DA
4
0.085
SIDE CHAIN
2
A
DA
5
0.069
SIDE CHAIN
3
A
DA
4
0.086
SIDE CHAIN
3
A
DA
5
0.064
SIDE CHAIN
4
A
DA
4
0.083
SIDE CHAIN
4
A
DA
5
0.064
SIDE CHAIN
5
A
DA
4
0.086
SIDE CHAIN
5
A
DA
5
0.059
SIDE CHAIN
5
A
DG
6
0.057
SIDE CHAIN
6
A
DA
4
0.080
SIDE CHAIN
6
A
DA
5
0.072
SIDE CHAIN
7
A
DA
4
0.082
SIDE CHAIN
7
A
DA
5
0.073
SIDE CHAIN
8
A
DA
4
0.074
SIDE CHAIN
8
A
DA
5
0.062
SIDE CHAIN
9
A
DA
4
0.082
SIDE CHAIN
9
A
DA
5
0.070
SIDE CHAIN
10
A
DA
4
0.088
SIDE CHAIN
10
A
DA
5
0.076
SIDE CHAIN
11
A
DA
4
0.083
SIDE CHAIN
11
A
DA
5
0.068
SIDE CHAIN
12
A
DA
4
0.079
SIDE CHAIN
12
A
DA
5
0.059
SIDE CHAIN
12
A
DG
6
0.060
SIDE CHAIN
13
A
DA
4
0.084
SIDE CHAIN
13
A
DA
5
0.072
SIDE CHAIN
14
A
DA
4
0.082
SIDE CHAIN
14
A
DA
5
0.071
SIDE CHAIN
1
1.82
0.30
108.30
110.12
A
A
A
O4'
C1'
N9
DG
DG
DG
1
1
1
N
1
2.44
0.30
108.30
110.74
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
1
3.30
0.50
117.70
121.00
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
1
-4.58
0.60
118.60
114.02
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
1
3.30
0.50
117.70
121.00
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
1
-4.26
0.60
118.60
114.34
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
1
4.94
0.30
108.30
113.24
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
1
2.06
0.30
108.30
110.36
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
2
2.54
0.30
108.30
110.84
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
2
3.15
0.50
117.70
120.85
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
2
-4.56
0.60
118.60
114.04
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
2
3.28
0.50
117.70
120.98
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
2
-4.26
0.60
118.60
114.34
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
2
2.95
0.30
108.30
111.25
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
3
1.89
0.30
108.30
110.19
A
A
A
O4'
C1'
N9
DG
DG
DG
1
1
1
N
3
2.07
0.30
108.30
110.37
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
3
3.34
0.50
117.70
121.04
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
3
-4.44
0.60
118.60
114.16
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
3
3.27
0.50
117.70
120.97
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
3
-4.19
0.60
118.60
114.41
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
3
3.77
0.30
108.30
112.07
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
4
3.12
0.30
108.30
111.42
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
4
3.25
0.50
117.70
120.95
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
4
-4.44
0.60
118.60
114.16
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
4
3.33
0.50
117.70
121.03
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
4
-4.34
0.60
118.60
114.26
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
4
3.36
0.30
108.30
111.66
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
5
2.25
0.30
108.30
110.55
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
5
3.25
0.50
117.70
120.95
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
5
-4.65
0.60
118.60
113.95
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
5
3.26
0.50
117.70
120.96
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
5
-4.10
0.60
118.60
114.50
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
5
4.31
0.30
108.30
112.61
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
6
1.80
0.30
108.30
110.10
A
A
A
O4'
C1'
N9
DG
DG
DG
1
1
1
N
6
2.19
0.30
108.30
110.49
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
6
3.20
0.50
117.70
120.90
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
6
-4.78
0.60
118.60
113.82
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
6
3.17
0.50
117.70
120.87
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
6
-4.19
0.60
118.60
114.41
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
6
3.54
0.30
108.30
111.84
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
7
2.09
0.30
108.30
110.39
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
7
3.23
0.50
117.70
120.93
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
7
-4.82
0.60
118.60
113.78
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
7
3.26
0.50
117.70
120.96
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
7
-4.31
0.60
118.60
114.29
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
7
2.97
0.30
108.30
111.27
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
8
1.85
0.30
108.30
110.15
A
A
A
O4'
C1'
N9
DG
DG
DG
1
1
1
N
8
3.24
0.30
108.30
111.54
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
8
3.26
0.50
117.70
120.96
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
8
-4.68
0.60
118.60
113.92
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
8
3.18
0.50
117.70
120.88
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
8
-4.15
0.60
118.60
114.45
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
8
2.95
0.30
108.30
111.25
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
9
2.65
0.30
108.30
110.95
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
9
3.15
0.50
117.70
120.85
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
9
-4.46
0.60
118.60
114.14
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
9
3.22
0.50
117.70
120.92
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
9
-4.24
0.60
118.60
114.36
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
9
3.52
0.30
108.30
111.82
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
10
1.80
0.30
108.30
110.10
A
A
A
O4'
C1'
N9
DG
DG
DG
1
1
1
N
10
3.17
0.50
117.70
120.87
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
10
-4.48
0.60
118.60
114.12
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
10
3.35
0.50
117.70
121.05
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
10
-4.23
0.60
118.60
114.37
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
10
3.58
0.30
108.30
111.88
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
11
2.83
0.30
108.30
111.13
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
11
3.27
0.50
117.70
120.97
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
11
-4.46
0.60
118.60
114.14
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
11
3.32
0.50
117.70
121.02
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
11
-4.23
0.60
118.60
114.37
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
11
2.84
0.30
108.30
111.14
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
12
2.88
0.30
108.30
111.18
A
A
A
O4'
C1'
N9
DG
DG
DG
1
1
1
N
12
2.05
0.30
108.30
110.35
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
12
3.28
0.50
117.70
120.98
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
12
-4.69
0.60
118.60
113.91
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
12
3.36
0.50
117.70
121.06
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
12
-4.33
0.60
118.60
114.27
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
12
4.40
0.30
108.30
112.70
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
12
1.90
0.30
108.30
110.20
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
13
2.02
0.30
108.30
110.32
A
A
A
O4'
C1'
N9
DG
DG
DG
1
1
1
N
13
2.18
0.30
108.30
110.48
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
13
3.20
0.50
117.70
120.90
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
13
-4.51
0.60
118.60
114.09
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
13
3.25
0.50
117.70
120.95
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
13
-4.25
0.60
118.60
114.35
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
13
2.74
0.30
108.30
111.04
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
14
1.82
0.30
108.30
110.12
A
A
A
O4'
C1'
N9
DG
DG
DG
1
1
1
N
14
2.41
0.30
108.30
110.71
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
14
3.26
0.50
117.70
120.96
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
14
-4.47
0.60
118.60
114.13
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
14
3.32
0.50
117.70
121.02
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
14
-4.30
0.60
118.60
114.30
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
14
3.29
0.30
108.30
111.59
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
REFINEMENT OF d(GCGAAGC) HAIRPIN STRUCTURE USING ONE- AND TWO-BOND RESIDUAL DIPOLAR COUPLINGS
1
N
N
hydrog
WATSON-CRICK
A
DG
1
A
N1
DG
1
1_555
A
DC
7
A
N3
DC
7
1_555
hydrog
WATSON-CRICK
A
DG
1
A
N2
DG
1
1_555
A
DC
7
A
O2
DC
7
1_555
hydrog
WATSON-CRICK
A
DG
1
A
O6
DG
1
1_555
A
DC
7
A
N4
DC
7
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N3
DC
2
1_555
A
DG
6
A
N1
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
A
DG
6
A
O6
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
A
DG
6
A
N2
DG
6
1_555
hydrog
TYPE_11_PAIR
A
DG
3
A
N2
DG
3
1_555
A
DA
5
A
N7
DA
5
1_555
hydrog
TYPE_11_PAIR
A
DG
3
A
N3
DG
3
1_555
A
DA
5
A
N6
DA
5
1_555
DNA
HAIRPIN, DNA, GA MISMATCH
1PQT
PDB
1
1PQT
1
7
1PQT
1
7
1PQT
A
1
1
7
1
P 1