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
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
10.2210/pdb2meq/pdb
pdb_00002meq
6077.673
RNA_(5'-R(P*GP*GP*CP*CP*GP*UP*AP*AP*CP*UP*AP*UP*AP*AP*CP*GP*GP*UP*C)-3')
1
syn
polymer
no
no
GGCCGUAACUAUAACGGUC
GGCCGUAACUAUAACGGUC
A
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-2.035
1
19
A
1
A
19
-0.383
A_G1:C19_A
1
-1.480
-0.400
-0.035
-0.164
-0.172
1
28
A
2
A
18
3.907
A_G2:U18_A
2
0.113
-2.083
-0.266
-0.268
2.542
1
19
A
3
A
17
2.601
A_C3:G17_A
3
-3.950
-0.140
0.004
-0.143
2.598
1
19
A
4
A
16
-3.314
A_C4:G16_A
4
2.239
0.535
-0.378
-0.236
-1.768
1
19
A
5
A
15
-1.626
A_G5:C15_A
5
-0.051
0.214
-0.169
-0.087
-11.138
A
6
A
13
-77.792
A_U6:A13_A
6
-2.340
1.652
-0.868
1.817
4.153
25.061
A
A
1
2
-11.797
A
A
19
18
4.018
-5.082
0.660
-1.305
AA_G1G2:U18C19_AA
1
-1.459
3.387
24.506
-1.108
-2.067
4.190
37.688
A
A
2
3
-13.032
A
A
18
17
4.065
-8.351
0.763
-1.180
AA_G2C3:G17U18_AA
2
-1.539
2.401
36.753
-0.442
-1.436
3.932
32.883
A
A
3
4
-5.001
A
A
17
16
3.947
-2.825
-1.120
-1.232
AA_C3C4:G16G17_AA
3
2.752
-4.872
32.652
-1.593
2.547
4.421
36.527
A
A
4
5
-37.632
A
A
16
15
4.951
-22.063
0.349
-0.728
AA_C4G5:C15G16_AA
4
-0.424
0.723
29.291
3.726
-0.650
6.440
51.213
A
A
5
6
-15.724
A
A
15
13
5.308
-13.173
-2.154
-3.642
AA_G5U6:A13C15_AA
5
-18.615
22.220
46.165
-2.481
0.044
database_2
pdbx_database_status
pdbx_nmr_software
pdbx_nmr_spectrometer
repository
Initial release
Database references
Database references
Data collection
Database references
Other
1
0
2014-01-01
1
1
2014-01-15
1
2
2014-04-16
1
3
2023-06-14
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.status_code_nmr_data
_pdbx_nmr_software.name
_pdbx_nmr_spectrometer.model
BMRB
Y
RCSB
2013-09-26
REL
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
2D 1H-13C HSQC
3D 1H-13C-1H HCCH-COSY
3D 1H-13C-1H HCCH-TOCSY
3D 1H-13C-13C HCCH-TOCSY
3D 1H-1H-13C NOESY-HMQC
1.0
mM
10
mM
50
mM
0.1
mM
1.0
mM
10
mM
50
mM
0.1
mM
1.0
mM
[U-100% 13C; U-100% 15N]
10
mM
50
mM
0.1
mM
70
7.3
ambient
298.2
K
simulated annealing, molecular dynamics, torsion angle dynamics
1
lowest energy
1.0 mM RNA (5'-P(GP*GP*CP*CP*GP*UP*AP*AP*CP*UP*AP*UP*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*UP*AP*AP*CP*UP*AP*UP*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
1.0 mM [U-100% 13C; U-100% 15N] RNA (5'-P(GP*GP*CP*CP*GP*UP*AP*AP*CP*UP*AP*UP*AP*AP*CP*GP*GP*UP*C)-3'), 10 mM Potassium Phosphate, 50 mM Potassium Chloride, 0.1 mM EDTA, 100% D2O
100% 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
U
6
n
6
U
6
A
A
7
n
7
A
7
A
A
8
n
8
A
8
A
C
9
n
9
C
9
A
U
10
n
10
U
10
A
A
11
n
11
A
11
A
U
12
n
12
U
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
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
lowest energy, model1
Structure of Helix 69 from Escherichia coli 23S Ribosomal RNA
1
N
N
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
U-A PAIR
A
U
6
A
O4
U
6
1_555
A
A
13
A
N6
A
13
1_555
hydrog
WATSON-CRICK
A
U
6
A
N3
U
6
1_555
A
A
14
A
N1
A
14
1_555
hydrog
WATSON-CRICK
A
U
6
A
O4
U
6
1_555
A
A
14
A
N6
A
14
1_555
RNA
Helix 69, Ribosomal, RNA
2MEQ
PDB
1
2MEQ
GGCCGUAACUAUAACGGUC
1
19
2MEQ
1
19
2MEQ
A
1
1
19