1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Leeper, T.C.
Schmidt, F.J.
Van Doren, S.R.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
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
US
Nat.Struct.Biol.
NSBIEW
2024
1072-8368
9
397
403
11927952
Structure of the UGAGAU hexaloop that braces Bacillus RNase P for action.
2002
10.2210/pdb1jp0/pdb
pdb_00001jp0
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
PL5.1 HAIRPIN FROM RNASE P RNA
6776.060
5'-R(*GP*GP*CP*GP*GP*UP*GP*CP*UP*GP*AP*GP*AP*UP*GP*CP*CP*CP*GP*UP*C)-3'
1
syn
polymer
no
no
GGCGGUGCUGAGAUGCCCGUC
GGCGGUGCUGAGAUGCCCGUC
A
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
0.135
1
19
A
1
A
21
7.767
A_G1:C21_A
1
-4.796
-1.390
-0.120
-0.448
0.604
28
A
2
A
20
-11.429
A_G2:U20_A
2
-9.245
-1.249
0.077
-0.292
4.030
1
19
A
3
A
19
2.724
A_C3:G19_A
3
2.058
0.109
-0.166
-0.194
-0.898
1
19
A
4
A
18
2.490
A_G4:C18_A
4
-7.837
-0.799
-0.130
-0.571
4.427
1
19
A
5
A
17
-5.800
A_G5:C17_A
5
6.517
-0.402
-0.521
-0.614
8.472
A
7
A
16
-11.967
A_G7:C16_A
6
-2.976
0.104
0.207
0.212
3.991
1
19
A
8
A
15
-2.714
A_C8:G15_A
7
-4.962
0.549
0.043
-0.371
3.555
28.538
A
A
1
2
-18.027
A
A
21
20
3.072
-8.748
-0.993
-2.014
AA_G1G2:U20C21_AA
1
-0.578
1.191
27.185
-2.017
1.878
3.725
36.065
A
A
2
3
-18.234
A
A
20
19
3.340
-11.106
0.743
-2.016
AA_G2C3:G19U20_AA
2
-2.750
4.514
34.259
-1.509
-1.633
2.610
26.931
A
A
3
4
11.022
A
A
19
18
3.030
5.083
-0.853
-2.493
AA_C3G4:C18G19_AA
3
-4.221
9.153
26.123
-6.492
0.884
2.581
44.115
A
A
4
5
39.469
A
A
18
17
2.772
27.548
-2.513
0.178
AA_G4G5:C17C18_AA
4
-5.241
7.508
34.404
-2.176
2.887
3.159
34.939
A
A
5
7
3.610
A
A
17
16
3.031
2.110
-1.180
-1.464
AA_G5G7:C16C17_AA
5
-13.845
23.686
32.090
-2.754
-0.107
2.153
30.979
A
A
7
8
24.529
A
A
16
15
3.134
12.724
-0.376
-1.819
AA_G7C8:G15C16_AA
6
-1.799
3.468
28.248
-5.487
0.409
database_2
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
1
0
2002-05-01
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
NMR structure of the LP5.1 hairpin from Bacillus RNase P RNA refined WITH residual dipolar couplings.
RCSB
Y
RCSB
2001-07-31
REL
REL
IN VITRO TRANSCRIPTION
sample
structures with the lowest energy
100
28
13C-separated-NOESY (Mixing times of 200 and 250 ms)
NOESY (Mixing times of 80 and 140 ms)
HCCH-TOCSY
HCCH-COSY
13C-Hetero-TOCSY
20 mM Sodium Phosphate
5.5
ambient
298
K
20 mM Sodium Phosphate
5.5
ambient
277
K
20 mM Sodium Phosphate
5.5
ambient
298
K
20 mM Sodium Phosphate
5.5
ambient
298
K
20 mM Sodium Phosphate
5.5
ambient
277
K
residual dipolar coupling refinement were NOT used for this structure, see 1JOX.
torsion angle dynamics
1
closest to the average
1.0 mM PL5.1 hairpin RNA U-15N,13C, 20mM phosphate buffer NA, 100% D2O
100% D2O
1.0 mM PL5.1 hairpin RNA U-15N,13C, 20mM phosphate buffer NA, 8% H2O 92% D2O
8% H2O 92% D2O
2.5 mM PL5.1 hairpin RNA U-15N,13C U and A residues only, 20mM phosphate buffer NA, 100% D2O
100% D2O
1.8 mM PL5.1 hairpin RNA U-15N,13C A, C, and G residues only, 20mM phosphate buffer NA, 100% D2O
100% D2O
1.8 mM PL5.1 hairpin RNA U-15N,13C A, C, and G residues only, 20mM phosphate buffer NA, 8% H2O 92% D2O
8% H2O 92% D2O
Brunger et. al
refinement
CNS
1.0
Brunger et. al
structure solution
CNS
1.0
500
Bruker
DRX
600
Varian
INOVA
G
1
n
1
G
1
A
G
2
n
2
G
2
A
C
3
n
3
C
3
A
G
4
n
4
G
4
A
G
5
n
5
G
5
A
U
6
n
6
U
6
A
G
7
n
7
G
7
A
C
8
n
8
C
8
A
U
9
n
9
U
9
A
G
10
n
10
G
10
A
A
11
n
11
A
11
A
G
12
n
12
G
12
A
A
13
n
13
A
13
A
U
14
n
14
U
14
A
G
15
n
15
G
15
A
C
16
n
16
C
16
A
C
17
n
17
C
17
A
C
18
n
18
C
18
A
G
19
n
19
G
19
A
U
20
n
20
U
20
A
C
21
n
21
C
21
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
A
H2'
O4'
U
G
14
15
1.34
1
A
A
HO2'
O5'
G
U
5
6
1.38
1
A
A
HO2'
O5'
G
A
12
13
1.40
1
A
A
N7
H5''
A
A
11
13
1.49
1
A
A
HO2'
O5'
G
G
4
5
1.52
1
A
A
H21
O2
G
C
4
18
1.55
1
A
A
O2
H21
C
G
3
19
1.56
2
A
A
H2'
O4'
U
G
14
15
1.42
2
A
A
H21
O2
G
C
4
18
1.53
2
A
A
HO2'
O4
U
U
9
14
1.55
2
A
A
O2
H21
C
G
3
19
1.57
2
A
A
H21
O2
G
C
5
17
1.58
2
A
A
O2'
HO2'
U
A
9
13
1.60
2
A
A
O2
H21
C
G
8
15
1.60
3
A
A
H2'
O4'
U
G
14
15
1.39
3
A
A
HO2'
O4
U
U
9
14
1.51
3
A
A
H21
O2
G
C
4
18
1.55
3
A
A
O2
H21
C
G
3
19
1.57
4
A
A
HO2'
O5'
G
U
5
6
1.35
4
A
A
H2'
O4'
U
G
14
15
1.37
4
A
A
H2'
O4'
C
U
8
9
1.52
4
A
A
HO2'
O5'
G
A
12
13
1.54
4
A
A
O2
H21
C
G
3
19
1.54
4
A
A
H21
O2
G
C
4
18
1.55
5
A
A
H2'
O4'
U
G
14
15
1.37
5
A
A
HO2'
O5'
G
U
5
6
1.40
5
A
A
H2'
O4'
C
U
8
9
1.48
5
A
A
HO2'
O5'
G
G
4
5
1.48
5
A
A
H21
O2
G
C
4
18
1.55
5
A
A
O2
H21
C
G
3
19
1.57
5
A
A
HO2'
O5'
G
A
12
13
1.57
6
A
A
H2'
O4'
U
G
14
15
1.40
6
A
A
H21
O2
G
C
4
18
1.55
6
A
A
O2
H21
C
G
3
19
1.56
6
A
A
HO2'
O5'
G
G
4
5
1.57
6
A
A
O6
H41
G
C
5
17
1.60
7
A
A
H2'
O4'
U
G
14
15
1.35
7
A
A
HO2'
O4
U
U
9
14
1.42
7
A
A
H2'
O4'
C
U
8
9
1.49
7
A
A
H21
O2
G
C
4
18
1.55
7
A
A
O2
H21
C
G
3
19
1.55
7
A
A
H21
O2
G
C
5
17
1.56
8
A
A
H2'
O4'
U
G
14
15
1.45
8
A
A
HO2'
O5'
G
G
4
5
1.52
8
A
A
H21
O2
G
C
4
18
1.53
8
A
A
H4'
O5'
G
U
5
6
1.55
8
A
A
O2
H21
C
G
3
19
1.57
8
A
A
HO2'
O4
U
U
9
14
1.58
9
A
A
H2'
O4'
U
G
14
15
1.38
9
A
A
H2'
O4'
C
U
8
9
1.46
9
A
A
HO2'
O5'
G
G
4
5
1.49
9
A
A
H4'
O5'
G
U
5
6
1.54
9
A
A
H21
O2
G
C
4
18
1.55
9
A
A
O2
H21
C
G
3
19
1.59
10
A
A
HO2'
O5'
G
U
5
6
1.32
10
A
A
H2'
O4'
U
G
14
15
1.34
10
A
A
HO2'
O5'
G
G
4
5
1.53
10
A
A
H21
O2
G
C
4
18
1.54
10
A
A
HO2'
O4
U
U
9
14
1.57
10
A
A
O2
H21
C
G
3
19
1.57
10
A
A
N7
H5''
A
A
11
13
1.58
11
A
A
H2'
O4'
U
G
14
15
1.36
11
A
A
O2'
H8
G
G
5
7
1.44
11
A
A
H21
O2
G
C
4
18
1.51
11
A
A
O2'
H5'
C
G
3
4
1.54
11
A
A
O2
H21
C
G
3
19
1.56
11
A
A
HO2'
O5'
G
A
12
13
1.56
11
A
A
H2'
O4'
C
U
8
9
1.59
12
A
A
HO2'
O5'
G
A
12
13
1.39
12
A
A
HO2'
O5'
G
G
4
5
1.47
12
A
A
H21
O2
G
C
4
18
1.53
12
A
A
H2'
O4'
U
G
14
15
1.54
12
A
A
O2
H21
C
G
3
19
1.56
12
A
A
H2'
O4'
C
U
8
9
1.58
13
A
A
H2'
O4'
U
G
14
15
1.35
13
A
A
HO2'
O5'
G
G
4
5
1.39
13
A
A
O2'
H3'
G
U
5
6
1.47
13
A
A
HO2'
O5'
G
U
5
6
1.50
13
A
A
H2'
O4'
C
U
8
9
1.55
13
A
A
H21
O2
G
C
4
18
1.55
13
A
A
H21
O2
G
C
5
17
1.57
14
A
A
H2'
O4'
U
G
14
15
1.31
14
A
A
H21
O2
G
C
4
18
1.54
14
A
A
HO2'
O5'
G
U
5
6
1.56
14
A
A
O2
H21
C
G
8
15
1.57
15
A
A
H2'
O4'
U
G
14
15
1.46
15
A
A
H21
O2
G
C
4
18
1.54
15
A
A
O2
H21
C
G
8
15
1.57
15
A
A
O2
H21
C
G
3
19
1.59
16
A
A
H2'
O4'
U
G
14
15
1.39
16
A
A
HO2'
O5'
G
A
12
13
1.42
16
A
A
H2'
O4'
C
U
8
9
1.52
16
A
A
HO2'
O4
U
U
9
14
1.52
16
A
A
N7
H5''
A
A
11
13
1.53
16
A
A
H21
O2
G
C
4
18
1.53
16
A
A
O2'
H5'
C
G
3
4
1.54
16
A
A
HO2'
O5'
U
G
6
7
1.55
16
A
A
O2
H21
C
G
3
19
1.56
16
A
A
O6
H41
G
C
5
17
1.60
17
A
A
H2'
O4'
U
G
14
15
1.40
17
A
A
O2'
H5'
C
G
3
4
1.45
17
A
A
H21
O2
G
C
4
18
1.53
17
A
A
H2'
O4'
C
U
8
9
1.56
17
A
A
O2
H21
C
G
3
19
1.56
17
A
A
H2'
O4'
C
C
17
18
1.58
17
A
A
N7
H5''
A
A
11
13
1.58
18
A
A
H2'
O4'
U
G
14
15
1.38
18
A
A
HO2'
O4
U
U
9
14
1.42
18
A
A
H2'
O4'
C
U
8
9
1.51
18
A
A
H21
O2
G
C
4
18
1.52
18
A
A
HO2'
O5'
G
U
5
6
1.58
18
A
A
HO2'
O5'
C
U
8
9
1.60
19
A
A
H2'
O4'
U
G
14
15
1.33
19
A
A
H21
O2
G
C
4
18
1.54
19
A
A
O2
H21
C
G
3
19
1.56
19
A
A
O2
H21
C
G
8
15
1.56
20
A
A
H2'
O4'
U
G
14
15
1.37
20
A
A
HO2'
O5'
G
U
5
6
1.40
20
A
A
O2'
H3'
G
U
5
6
1.54
20
A
A
H21
O2
G
C
4
18
1.54
20
A
A
H2'
O4'
C
U
8
9
1.55
20
A
A
H2'
O4'
G
C
15
16
1.56
20
A
A
HO2'
O5'
G
A
12
13
1.57
20
A
A
HO2'
O5'
U
G
6
7
1.58
20
A
A
O2
H21
C
G
3
19
1.60
21
A
A
H2'
O4'
U
G
14
15
1.37
21
A
A
O2'
H5'
C
G
3
4
1.46
21
A
A
HO2'
O5'
G
U
5
6
1.48
21
A
A
H2'
O4'
C
U
8
9
1.50
21
A
A
H21
O2
G
C
4
18
1.53
21
A
A
O2
H21
C
G
3
19
1.54
21
A
A
H21
O2
G
C
5
17
1.54
21
A
A
H21
O2
G
C
1
21
1.58
22
A
A
H2'
O4'
U
G
14
15
1.35
22
A
A
O2'
H5'
C
G
3
4
1.45
22
A
A
H21
O2
G
C
4
18
1.53
22
A
A
O4'
H6
G
U
5
6
1.56
22
A
A
O2
H21
C
G
3
19
1.56
22
A
A
H2'
N7
G
G
4
5
1.58
23
A
A
H2'
O4'
U
G
14
15
1.42
23
A
A
H2'
O4'
C
U
8
9
1.50
23
A
A
H21
O2
G
C
4
18
1.55
23
A
A
N7
H5''
A
A
11
13
1.55
23
A
A
O2
H21
C
G
3
19
1.57
23
A
A
H2'
O4'
C
C
17
18
1.58
23
A
A
H4'
O5'
G
U
5
6
1.60
24
A
A
H2'
O4'
U
G
14
15
1.40
24
A
A
H2'
O4'
C
U
8
9
1.43
24
A
A
HO2'
O5'
G
U
5
6
1.49
24
A
A
H21
O2
G
C
4
18
1.53
24
A
A
O3'
H8
G
G
4
5
1.55
24
A
A
HO2'
O5'
U
G
6
7
1.56
24
A
A
HO2'
O4
U
U
9
14
1.58
25
A
A
HO2'
O5'
G
A
12
13
1.38
25
A
A
H2'
O4'
C
U
8
9
1.46
25
A
A
N7
H5''
A
A
11
13
1.46
25
A
A
HO2'
O5'
G
U
5
6
1.46
25
A
A
H2'
O4'
U
G
14
15
1.48
25
A
A
HO2'
O5'
G
G
4
5
1.49
25
A
A
O2
H21
C
G
3
19
1.56
25
A
A
H21
O2
G
C
4
18
1.57
26
A
A
H2'
O4'
U
G
14
15
1.31
26
A
A
H2'
O4'
C
U
8
9
1.46
26
A
A
HO2'
O4
U
U
9
14
1.53
26
A
A
H21
O2
G
C
4
18
1.55
26
A
A
H21
O2
G
C
7
16
1.58
26
A
A
H21
O2
G
C
1
21
1.59
26
A
A
HO2'
O5'
C
U
8
9
1.60
27
A
A
H2'
O4'
C
U
8
9
1.45
27
A
A
H2'
O4'
U
G
14
15
1.51
27
A
A
HO2'
O5'
G
G
4
5
1.52
27
A
A
H21
O2
G
C
4
18
1.55
27
A
A
H8
O3'
G
A
10
13
1.60
28
A
A
H2'
O4'
U
G
14
15
1.36
28
A
A
HO2'
O5'
G
A
12
13
1.44
28
A
A
H21
O2
G
C
4
18
1.52
28
A
A
O2
H21
C
G
3
19
1.57
28
A
A
N7
H5''
A
A
11
13
1.57
28
A
A
HO2'
O4
U
U
9
14
1.58
20
A
C
21
0.068
SIDE CHAIN
21
A
C
21
0.062
SIDE CHAIN
25
A
G
5
0.059
SIDE CHAIN
28
A
U
9
0.084
SIDE CHAIN
26
9.88
1.30
114.00
123.88
A
A
A
N9
C1'
C2'
A
A
A
13
13
13
N
NMR Structure of the LP5.1 Hairpin from Bacillus RNase P RNA Refined WITHOUT Residual Dipolar Couplings
1
N
N
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
A
C
21
A
N3
C
21
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
A
C
21
A
O2
C
21
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
A
C
21
A
N4
C
21
1_555
hydrog
TYPE_28_PAIR
A
G
2
A
N1
G
2
1_555
A
U
20
A
O2
U
20
1_555
hydrog
TYPE_28_PAIR
A
G
2
A
O6
G
2
1_555
A
U
20
A
N3
U
20
1_555
hydrog
WATSON-CRICK
A
C
3
A
N3
C
3
1_555
A
G
19
A
N1
G
19
1_555
hydrog
WATSON-CRICK
A
C
3
A
N4
C
3
1_555
A
G
19
A
O6
G
19
1_555
hydrog
WATSON-CRICK
A
C
3
A
O2
C
3
1_555
A
G
19
A
N2
G
19
1_555
hydrog
WATSON-CRICK
A
G
4
A
N1
G
4
1_555
A
C
18
A
N3
C
18
1_555
hydrog
WATSON-CRICK
A
G
4
A
N2
G
4
1_555
A
C
18
A
O2
C
18
1_555
hydrog
WATSON-CRICK
A
G
4
A
O6
G
4
1_555
A
C
18
A
N4
C
18
1_555
hydrog
WATSON-CRICK
A
G
5
A
N1
G
5
1_555
A
C
17
A
N3
C
17
1_555
hydrog
WATSON-CRICK
A
G
5
A
N2
G
5
1_555
A
C
17
A
O2
C
17
1_555
hydrog
WATSON-CRICK
A
G
5
A
O6
G
5
1_555
A
C
17
A
N4
C
17
1_555
hydrog
G-C PAIR
A
G
7
A
N1
G
7
1_555
A
C
16
A
N3
C
16
1_555
hydrog
WATSON-CRICK
A
C
8
A
N3
C
8
1_555
A
G
15
A
N1
G
15
1_555
hydrog
WATSON-CRICK
A
C
8
A
N4
C
8
1_555
A
G
15
A
O6
G
15
1_555
hydrog
WATSON-CRICK
A
C
8
A
O2
C
8
1_555
A
G
15
A
N2
G
15
1_555
RNA
RIBONUCLEIC ACID, RNASE P, HAIRPIN, RESIDUAL DIPOLAR COUPLING REFINEMENT, UGNRAU, RNA
1JP0
PDB
1
1JP0
1
21
1JP0
1
21
1JP0
A
1
1
21