1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Jiang, J.
Aduri, R.
Chow, C.S.
Santalucia, J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C10 H14 N5 O7 P
347.221
y
ADENOSINE-5'-MONOPHOSPHATE
RNA linking
C9 H14 N3 O8 P
323.197
y
CYTIDINE-5'-MONOPHOSPHATE
RNA linking
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA linking
C9 H13 N2 O9 P
324.181
n
PSEUDOURIDINE-5'-MONOPHOSPHATE
RNA linking
C9 H13 N2 O9 P
324.181
y
URIDINE-5'-MONOPHOSPHATE
RNA linking
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
42
3971
3981
10.1093/nar/gkt1329
24371282
Structure modulation of helix 69 from Escherichia coli 23S ribosomal RNA by pseudouridylations.
2014
6077.673
RNA_(5'-R(P*GP*GP*CP*CP*GP*(PSU)P*AP*AP*CP*(PSU)P*AP*(PSU)P*AP*AP*CP*GP*GP*UP*C)-3')
1
syn
polymer
no
yes
GGCCG(PSU)AAC(PSU)A(PSU)AACGGUC
GGCCGUAACUAUAACGGUC
A
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
2.359
1
19
A
1
A
19
-8.118
A_G1:C19_A
1
1.988
0.290
0.015
-0.242
1.806
1
28
A
2
A
18
-1.392
A_G2:U18_A
2
-1.428
-2.020
-0.076
-0.292
1.759
1
19
A
3
A
17
1.839
A_C3:G17_A
3
-2.505
-0.232
-0.047
-0.121
6.787
1
19
A
4
A
16
0.669
A_C4:G16_A
4
4.416
0.016
-0.321
-0.244
-1.109
1
19
A
5
A
15
-5.546
A_G5:C15_A
5
0.386
-0.225
-0.193
-0.176
-0.458
1
21
A
6
A
14
-12.254
A_PSU6:A14_A
6
-4.209
-0.271
0.036
-0.265
30.204
1
A
8
A
12
37.321
A_A8:PSU12_A
7
-3.382
0.064
2.091
0.660
3.789
21.088
A
A
1
2
-9.222
A
A
19
18
3.498
-3.361
0.276
-2.111
AA_G1G2:U18C19_AA
1
0.200
-0.549
20.820
-4.190
-0.660
4.205
37.124
A
A
2
3
-11.336
A
A
18
17
4.051
-7.174
0.134
-1.200
AA_G2C3:G17U18_AA
2
0.486
-0.767
36.445
-0.664
-0.129
4.072
36.259
A
A
3
4
-12.528
A
A
17
16
3.965
-7.731
0.800
-0.673
AA_C3C4:G16G17_AA
3
3.198
-5.182
35.313
0.269
-0.728
4.552
27.689
A
A
4
5
-18.033
A
A
16
15
4.460
-8.494
-1.166
-1.168
AA_C4G5:C15G16_AA
4
1.172
-2.489
26.353
0.466
2.838
3.778
25.060
A
A
5
6
-2.115
A
A
15
14
3.767
-0.914
0.042
-1.839
AA_G5PSU6:A14C15_AA
5
-3.938
9.113
24.737
-3.923
-1.451
repository
Initial release
Database references
Database references
1
0
2014-01-01
1
1
2014-01-15
1
2
2014-04-16
BMRB
Y
RCSB
2013-09-26
REL
REL
REL
CONVERGED LOWEST ENERGY STRUCTURES
100
10
2D 1H-13C NATURAL ABUNDANCE HMQC
2D 1H-1H NOESY
2D DQF-COSY
3D 1H-1H-1H TOCSY-NOESY
2D 1H-31P HETCOR
1D 31P
2D 1H-1H NOESY
1.0
mM
10
mM
50
mM
0.1
mM
1.0
mM
10
mM
50
mM
0.1
mM
70
7.3
ambient
310.2
K
70
7.3
ambient
283.2
K
simulated annealing, molecular dynamics, torsion angle dynamics
1
lowest energy
1.0 mM RNA (5'-P(GP*GP*CP*CP*GP*(PSU)P*AP*AP*CP*(PSU)P*AP*(PSU)P*AP*AP*CP*GP*GP*UP*C)-3'), 10 mM Potassium Phosphate, 50 mM Potassium Chloride, 0.1 mM EDTA, 100% D2O
100% D2O
1.0 mM RNA (5'-P(GP*GP*CP*CP*GP*(PSU)P*AP*AP*CP*(PSU)P*AP*(PSU)P*AP*AP*CP*GP*GP*UP*C)-3'), 10 mM Potassium Phosphate, 50 mM Potassium Chloride, 0.1 mM EDTA, 90% H2O/10% D2O
90% H2O/10% D2O
Goddard
chemical shift assignment
SPARKY
Goddard
data analysis
SPARKY
Brunger, Adams, Clore, Gros, Nilges and Read
structure solution
CNS
1.2
Brunger, Adams, Clore, Gros, Nilges and Read
refinement
CNS
1.2
Bruker Biospin
collection
TOPSPIN
Bruker Biospin
processing
TOPSPIN
700
Bruker
Avance
Bruker Avance
400
Varian
Mercury
Varian Mercury
G
1
n
1
G
1
A
G
2
n
2
G
2
A
C
3
n
3
C
3
A
C
4
n
4
C
4
A
G
5
n
5
G
5
A
PSU
6
n
6
PSU
6
A
A
7
n
7
A
7
A
A
8
n
8
A
8
A
C
9
n
9
C
9
A
PSU
10
n
10
PSU
10
A
A
11
n
11
A
11
A
PSU
12
n
12
PSU
12
A
A
13
n
13
A
13
A
A
14
n
14
A
14
A
C
15
n
15
C
15
A
G
16
n
16
G
16
A
G
17
n
17
G
17
A
U
18
n
18
U
18
A
C
19
n
19
C
19
A
author_defined_assembly
1
monomeric
A
PSU
6
PSEUDOURIDINE-5'-MONOPHOSPHATE
A
PSU
6
U
A
PSU
10
PSEUDOURIDINE-5'-MONOPHOSPHATE
A
PSU
10
U
A
PSU
12
PSEUDOURIDINE-5'-MONOPHOSPHATE
A
PSU
12
U
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
O2
H61
PSU
A
6
14
1.49
1
A
A
O6
H41
G
C
1
19
1.52
1
A
A
O2
H21
C
G
4
16
1.60
2
A
A
O6
H41
G
C
1
19
1.51
3
A
A
O6
H41
G
C
1
19
1.49
4
A
A
O6
H41
G
C
1
19
1.51
5
A
A
O2
H61
PSU
A
6
14
1.49
5
A
A
O2'
O4'
A
PSU
11
12
1.79
6
A
A
O2
H61
PSU
A
6
14
1.50
6
A
A
O6
H41
G
C
1
19
1.51
6
A
A
O2'
O4'
A
PSU
11
12
1.77
7
A
A
O6
H41
G
C
1
19
1.52
8
A
A
O2
H61
PSU
A
6
14
1.49
8
A
A
O6
H41
G
C
1
19
1.51
8
A
A
O2
H21
C
G
4
16
1.60
8
A
A
O2'
O4'
A
PSU
11
12
1.79
9
A
A
O6
H41
G
C
1
19
1.51
10
A
A
O2
H61
PSU
A
6
14
1.51
10
A
A
O6
H41
G
C
1
19
1.52
10
A
A
O2
H21
C
G
4
16
1.60
5'-R(P*GP*GP*CP*CP*GP*(PSU)P*AP*AP*CP*(PSU)P*AP*(PSU)P*AP*AP*CP*GP*GP*UP*C)-3'
lowest energy, model1
Structure of helix 69 from escherichia coli 23s ribosomal rna
1
N
N
covale
1.610
A
G
5
A
O3'
G
5
1_555
A
PSU
6
A
P
PSU
6
1_555
covale
1.607
A
PSU
6
A
O3'
PSU
6
1_555
A
A
7
A
P
A
7
1_555
covale
1.612
A
C
9
A
O3'
C
9
1_555
A
PSU
10
A
P
PSU
10
1_555
covale
1.609
A
PSU
10
A
O3'
PSU
10
1_555
A
A
11
A
P
A
11
1_555
covale
1.607
A
A
11
A
O3'
A
11
1_555
A
PSU
12
A
P
PSU
12
1_555
covale
1.609
A
PSU
12
A
O3'
PSU
12
1_555
A
A
13
A
P
A
13
1_555
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
A
C
19
A
N3
C
19
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
A
C
19
A
O2
C
19
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
A
C
19
A
N4
C
19
1_555
hydrog
TYPE_28_PAIR
A
G
2
A
N1
G
2
1_555
A
U
18
A
O2
U
18
1_555
hydrog
TYPE_28_PAIR
A
G
2
A
O6
G
2
1_555
A
U
18
A
N3
U
18
1_555
hydrog
WATSON-CRICK
A
C
3
A
N3
C
3
1_555
A
G
17
A
N1
G
17
1_555
hydrog
WATSON-CRICK
A
C
3
A
N4
C
3
1_555
A
G
17
A
O6
G
17
1_555
hydrog
WATSON-CRICK
A
C
3
A
O2
C
3
1_555
A
G
17
A
N2
G
17
1_555
hydrog
WATSON-CRICK
A
C
4
A
N3
C
4
1_555
A
G
16
A
N1
G
16
1_555
hydrog
WATSON-CRICK
A
C
4
A
N4
C
4
1_555
A
G
16
A
O6
G
16
1_555
hydrog
WATSON-CRICK
A
C
4
A
O2
C
4
1_555
A
G
16
A
N2
G
16
1_555
hydrog
WATSON-CRICK
A
G
5
A
N1
G
5
1_555
A
C
15
A
N3
C
15
1_555
hydrog
WATSON-CRICK
A
G
5
A
N2
G
5
1_555
A
C
15
A
O2
C
15
1_555
hydrog
WATSON-CRICK
A
G
5
A
O6
G
5
1_555
A
C
15
A
N4
C
15
1_555
hydrog
REVERSED WATSON-CRICK
A
PSU
6
A
N3
PSU
6
1_555
A
A
14
A
N1
A
14
1_555
hydrog
REVERSED WATSON-CRICK
A
PSU
6
A
O2
PSU
6
1_555
A
A
14
A
N6
A
14
1_555
hydrog
A-PSU MISPAIR
A
A
8
A
N1
A
8
1_555
A
PSU
12
A
N3
PSU
12
1_555
RNA
Pseudouridine, Helix 69, Ribosomal, RNA
2MER
PDB
1
2MER
GGCCGUAACUAUAACGGUC
1
19
2MER
1
19
2MER
A
1
1
19