1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Schmitz, M.
Tinoco Jr., I.
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 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
RNA
RNARFU
2122
1355-8382
6
1212
1225
10.1017/S1355838200000881
10999599
Solution structure and metal-ion binding of the P4 element from bacterial RNase P RNA.
2000
10.2210/pdb1f6x/pdb
pdb_00001f6x
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
8633.143
RNASE P RNA RIBOZYME, P4 DOMAIN
P4 STEM
1
syn
polymer
no
no
GGAAGUCCGGUCUUCGGACCGGCUUCC
GGAAGUCCGGUCUUCGGACCGGCUUCC
A
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
45.429
1
19
A
1
A
27
-1.594
A_G1:C27_A
1
13.442
-0.073
-0.447
-0.357
3.832
1
19
A
2
A
26
-7.953
A_G2:C26_A
2
-13.694
-0.263
0.367
-0.318
-3.680
1
20
A
3
A
25
-6.315
A_A3:U25_A
3
-27.087
0.057
-0.288
-0.218
1.189
1
20
A
4
A
24
-3.277
A_A4:U24_A
4
-3.902
0.035
-0.544
-0.032
3.569
1
19
A
5
A
23
-3.362
A_G5:C23_A
5
-2.771
-0.265
-0.717
-0.288
-7.523
1
19
A
7
A
22
-1.490
A_C7:G22_A
6
22.793
0.184
0.301
-0.041
-16.224
1
19
A
8
A
21
-7.479
A_C8:G21_A
7
6.319
-0.044
-0.566
-0.331
5.116
1
19
A
9
A
20
-3.282
A_G9:C20_A
8
-1.410
-0.074
-0.448
-0.255
1.824
1
19
A
10
A
19
9.722
A_G10:C19_A
9
-17.560
-0.374
-1.213
-0.693
5.860
1
20
A
11
A
18
-3.791
A_U11:A18_A
10
-4.862
-0.257
-0.598
0.012
-31.562
1
19
A
12
A
17
-3.886
A_C12:G17_A
11
18.315
0.241
1.929
-0.605
37.427
2
A
13
A
16
-64.645
A_U13:G16_A
12
9.967
1.250
0.239
-5.438
4.050
35.173
A
A
1
2
40.347
A
A
27
26
5.665
22.491
-0.958
-0.674
AA_G1G2:C26C27_AA
1
-4.437
7.960
26.857
-6.821
0.459
3.129
36.654
A
A
2
3
19.695
A
A
26
25
3.733
12.142
0.162
-1.249
AA_G2A3:U25C26_AA
2
4.011
-6.506
34.423
-3.792
0.338
3.863
33.718
A
A
3
4
-10.768
A
A
25
24
3.743
-6.212
0.597
-1.035
AA_A3A4:U24U25_AA
3
-0.252
0.437
33.156
-0.600
-1.078
2.490
30.279
A
A
4
5
31.348
A
A
24
23
3.689
15.617
-0.131
-1.356
AA_A4G5:C23U24_AA
4
0.521
-1.046
26.017
-5.816
0.358
3.364
60.484
A
A
5
7
30.664
A
A
23
22
3.603
29.516
-2.212
-0.493
AA_G5C7:G22C23_AA
5
-13.860
14.399
51.657
-2.173
1.405
3.830
35.118
A
A
7
8
20.123
A
A
22
21
4.641
11.874
-1.184
-1.031
AA_C7C8:G21G22_AA
6
5.054
-8.566
32.730
-4.096
2.979
2.980
26.741
A
A
8
9
13.308
A
A
21
20
3.234
6.102
0.247
-0.745
AA_C8G9:C20G21_AA
7
-0.487
1.063
26.043
-3.138
-0.657
3.683
31.387
A
A
9
10
21.151
A
A
20
19
4.056
11.146
0.777
-0.544
AA_G9G10:C19C20_AA
8
5.395
-10.237
28.898
-3.592
-0.184
2.170
39.219
A
A
10
11
34.776
A
A
19
18
3.195
21.998
-0.892
-1.081
AA_G10U11:A18C19_AA
9
-5.280
8.347
32.248
-3.999
0.755
2.346
40.921
A
A
11
12
33.511
A
A
18
17
4.397
21.301
-0.618
-2.238
AA_U11C12:G17A18_AA
10
-19.217
30.231
29.493
-6.041
-1.679
2.124
99.581
A
A
12
13
-0.381
A
A
17
16
2.498
-0.579
2.012
-2.103
AA_C12U13:G16G17_AA
11
-22.973
15.115
97.585
-1.371
-1.579
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2000-10-09
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
THE WILDTYPE P4 STEM OLIGORIBONUCLEOTIDE COMPLEXED WITH COBALT (III) HEXAMMINE
THE C70U MUTANT P4 STEM OLIGORIBONUCLEOTIDE
RCSB
Y
RCSB
2000-06-23
REL
REL
synthesized from DNA oligonucleotide template by T7 RNA polymerase
sample
This structure was determined using standard 2D homonuclear techniques and 13C and 31P heteronuclear techniques at natural abundance
1
2D NOESY
2D NOESY
2D NOESY
2D NOESY
DQF-COSY
31P-1H-COSY
13C-1H-HMQC
100 mM Na
6.5
ambient
288
K
100 mM Na
6.5
ambient
288
K
100 mM Na, 10 mM Mg
6.5
ambient
288
K
100 mM Na, 3 mM Co(NH3)6
6.5
ambient
288
K
The average structure is based on superposition of nine converged structures after refinement. The average RMS deviation between the ensemble and the average structure is 1.8 Angstrom. A total of 266 NOE-derived distance constraints, 164 dihedral restraints and 48 distance restraints from hydrogen bonds were used in the refinement
restrained molecular dynamics; simulated annealing
1
minimized average structure
2 mM P4 RNA; 100 mM sodium chloride; 10 mM phosphate buffer; 90% H2O, 10% D2O
90% H2O/10% D2O
2 mM P4 RNA; 100 mM sodium chloride; 10 mM phosphate buffer; 99.96% D2O
99.96% D2O
2 mM P4 RNA; 100 mM sodium chloride; 10 mM magnesium chloride; 10 mM phosphate buffer; 90% H2O, 10% D2O
90% H2O/10% D2O
2 mM P4 RNA; 100 mM sodium chloride; 3 mM hexammine cobalt chloride; 10 mM phosphate buffer; 90% H2O, 10% D2O
90% H2O/10% D2O
Bruker
collection
XwinNMR
3.1
MSI
processing
Felix
95.0
Brunger
structure solution
X-PLOR
3.841
Brunger
refinement
X-PLOR
3.841
600
Bruker
AMX
500
Bruker
DRX
G
1
n
1
G
1
A
G
2
n
2
G
2
A
A
3
n
3
A
3
A
A
4
n
4
A
4
A
G
5
n
5
G
5
A
U
6
n
6
U
6
A
C
7
n
7
C
7
A
C
8
n
8
C
8
A
G
9
n
9
G
9
A
G
10
n
10
G
10
A
U
11
n
11
U
11
A
C
12
n
12
C
12
A
U
13
n
13
U
13
A
U
14
n
14
U
14
A
C
15
n
15
C
15
A
G
16
n
16
G
16
A
G
17
n
17
G
17
A
A
18
n
18
A
18
A
C
19
n
19
C
19
A
C
20
n
20
C
20
A
G
21
n
21
G
21
A
G
22
n
22
G
22
A
C
23
n
23
C
23
A
U
24
n
24
U
24
A
U
25
n
25
U
25
A
C
26
n
26
C
26
A
C
27
n
27
C
27
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
minimized average
SOLUTION STRUCTURE OF THE RNASE P RNA (M1 RNA) P4 STEM OLIGORIBONUCLEOTIDE
1
N
N
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
A
C
27
A
N3
C
27
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
A
C
27
A
O2
C
27
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
A
C
27
A
N4
C
27
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
A
C
26
A
N3
C
26
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
A
C
26
A
O2
C
26
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
A
C
26
A
N4
C
26
1_555
hydrog
WATSON-CRICK
A
A
3
A
N1
A
3
1_555
A
U
25
A
N3
U
25
1_555
hydrog
WATSON-CRICK
A
A
3
A
N6
A
3
1_555
A
U
25
A
O4
U
25
1_555
hydrog
WATSON-CRICK
A
A
4
A
N1
A
4
1_555
A
U
24
A
N3
U
24
1_555
hydrog
WATSON-CRICK
A
A
4
A
N6
A
4
1_555
A
U
24
A
O4
U
24
1_555
hydrog
WATSON-CRICK
A
G
5
A
N1
G
5
1_555
A
C
23
A
N3
C
23
1_555
hydrog
WATSON-CRICK
A
G
5
A
N2
G
5
1_555
A
C
23
A
O2
C
23
1_555
hydrog
WATSON-CRICK
A
G
5
A
O6
G
5
1_555
A
C
23
A
N4
C
23
1_555
hydrog
WATSON-CRICK
A
C
7
A
N3
C
7
1_555
A
G
22
A
N1
G
22
1_555
hydrog
WATSON-CRICK
A
C
7
A
N4
C
7
1_555
A
G
22
A
O6
G
22
1_555
hydrog
WATSON-CRICK
A
C
7
A
O2
C
7
1_555
A
G
22
A
N2
G
22
1_555
hydrog
WATSON-CRICK
A
C
8
A
N3
C
8
1_555
A
G
21
A
N1
G
21
1_555
hydrog
WATSON-CRICK
A
C
8
A
N4
C
8
1_555
A
G
21
A
O6
G
21
1_555
hydrog
WATSON-CRICK
A
C
8
A
O2
C
8
1_555
A
G
21
A
N2
G
21
1_555
hydrog
WATSON-CRICK
A
G
9
A
N1
G
9
1_555
A
C
20
A
N3
C
20
1_555
hydrog
WATSON-CRICK
A
G
9
A
N2
G
9
1_555
A
C
20
A
O2
C
20
1_555
hydrog
WATSON-CRICK
A
G
9
A
O6
G
9
1_555
A
C
20
A
N4
C
20
1_555
hydrog
WATSON-CRICK
A
G
10
A
N1
G
10
1_555
A
C
19
A
N3
C
19
1_555
hydrog
WATSON-CRICK
A
G
10
A
N2
G
10
1_555
A
C
19
A
O2
C
19
1_555
hydrog
WATSON-CRICK
A
G
10
A
O6
G
10
1_555
A
C
19
A
N4
C
19
1_555
hydrog
WATSON-CRICK
A
U
11
A
N3
U
11
1_555
A
A
18
A
N1
A
18
1_555
hydrog
WATSON-CRICK
A
U
11
A
O4
U
11
1_555
A
A
18
A
N6
A
18
1_555
hydrog
WATSON-CRICK
A
C
12
A
N3
C
12
1_555
A
G
17
A
N1
G
17
1_555
hydrog
WATSON-CRICK
A
C
12
A
N4
C
12
1_555
A
G
17
A
O6
G
17
1_555
hydrog
WATSON-CRICK
A
C
12
A
O2
C
12
1_555
A
G
17
A
N2
G
17
1_555
hydrog
U-G MISPAIR
A
U
13
A
O2
U
13
1_555
A
G
16
A
N1
G
16
1_555
RNA
RIBONUCLEASE P, RIBOZYME, TRANSFER RNA PROCESSING, P4 STEM, METAL BINDING SITE, RNA
1F6X
PDB
1
1F6X
1
27
1F6X
1
27
1F6X
A
1
1
27
1
P 1