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/pdb1f6z/pdb
pdb_00001f6z
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
8634.127
RNASE P RNA RIBOZYME, P4 DOMAIN MUTANT
P4 STEM
C70U
1
syn
polymer
no
no
GGAAGUUCGGUCUUCGGACCGGCUUCC
GGAAGUUCGGUCUUCGGACCGGCUUCC
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
60.648
1
19
A
1
A
27
-3.522
A_G1:C27_A
1
18.925
-0.056
-0.009
-0.141
18.692
1
19
A
2
A
26
-10.549
A_G2:C26_A
2
1.795
-0.053
1.590
-0.562
13.278
1
20
A
3
A
25
-7.827
A_A3:U25_A
3
-17.077
-0.026
0.094
-0.159
2.460
1
20
A
4
A
24
-0.112
A_A4:U24_A
4
-13.001
0.003
-0.720
-0.125
-6.799
1
19
A
5
A
23
-1.792
A_G5:C23_A
5
-29.002
-0.206
-0.158
-0.256
-16.733
28
A
6
A
22
-7.820
A_U6:G22_A
6
3.955
2.075
1.081
-0.671
-26.763
1
19
A
8
A
21
-10.282
A_C8:G21_A
7
14.205
-0.064
-1.154
-0.898
3.058
1
19
A
9
A
20
-4.729
A_G9:C20_A
8
-2.272
0.054
1.457
-0.751
-2.253
1
19
A
10
A
19
8.102
A_G10:C19_A
9
-26.447
-0.397
-0.791
-0.460
-0.775
1
20
A
11
A
18
-10.453
A_U11:A18_A
10
-1.209
-0.110
-1.587
-0.769
-7.798
1
19
A
12
A
17
0.267
A_C12:G17_A
11
-7.953
0.513
-0.400
-0.302
27.077
6
A
13
A
16
-75.546
A_U13:G16_A
12
-6.454
1.320
-0.436
-5.494
4.186
29.596
A
A
1
2
35.649
A
A
27
26
5.881
16.824
-1.331
-1.347
AA_G1G2:C26C27_AA
1
-8.848
18.747
22.790
-8.869
-0.672
2.594
42.302
A
A
2
3
24.725
A
A
26
25
3.640
17.228
-0.050
-1.679
AA_G2A3:U25C26_AA
2
9.017
-12.940
37.751
-4.114
1.005
4.785
35.221
A
A
3
4
-17.333
A
A
25
24
4.708
-10.317
0.989
-0.661
AA_A3A4:U24U25_AA
3
4.365
-7.334
33.445
1.196
-0.666
4.005
31.638
A
A
4
5
3.479
A
A
24
23
4.076
1.896
0.199
-1.054
AA_A4G5:C23U24_AA
4
-0.263
0.483
31.581
-2.367
-0.426
2.677
50.784
A
A
5
6
32.241
A
A
23
22
3.718
26.403
0.445
-0.997
AA_G5U6:G22C23_AA
5
-5.089
6.214
43.488
-3.141
-0.901
1.716
44.968
A
A
6
8
54.773
A
A
22
21
4.643
35.397
0.633
-1.267
AA_U6C8:G21G22_AA
6
15.200
-23.520
23.652
-5.855
0.976
1.754
34.385
A
A
8
9
14.840
A
A
21
20
2.550
8.536
0.821
-1.382
AA_C8G9:C20G21_AA
7
-10.968
19.068
31.529
-3.256
-2.567
3.911
35.446
A
A
9
10
12.004
A
A
20
19
4.063
7.018
1.000
-0.522
AA_G9G10:C19C20_AA
8
15.696
-26.847
31.114
-2.201
1.364
3.699
30.100
A
A
10
11
11.985
A
A
19
18
3.875
6.182
-1.365
-0.583
AA_G10U11:A18C19_AA
9
-0.467
0.904
29.469
-2.603
2.516
2.325
42.333
A
A
11
12
40.143
A
A
18
17
3.801
26.878
0.083
-1.032
AA_U11C12:G17A18_AA
10
-3.950
5.900
32.778
-4.369
-0.547
3.233
105.621
A
A
12
13
1.214
A
A
17
16
3.610
1.928
2.307
-1.610
AA_C12U13:G16G17_AA
11
-20.798
13.096
104.149
-1.038
-1.749
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
1F6X shows the structure of the wildtype P4 stem oligoribonucleotide; in the wildtype the universally conserved U69 occupies the bulged position found for U70 in the mutant
RCSB
Y
RCSB
2000-06-24
REL
REL
synthesized from DNA oligonucleotide template by T7 RNA polymerase
sample
This structure was determined using standard 2D homonuclear techniques as well as 13C and 31P heteronuclear experiments at natural isotope 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 17 converged structures after refinement. The average RMS deviation between the ensemble and the average structure is 1.9 Angstrom. A total of 268 NOE derived distance constraints, 171 dihedral restraints and 49 distance restraints from hydrogen bonds were used for refinement
restrained molecular dynamics and simulated annealing
1
minimized average structure
2 mM P4m RNA; 100 mM sodium chloride; 10 mM phosphate buffer; 90% H2O, 10% D2O
90% H2O/10% D2O
2 mM P4m RNA; 100 mM sodium chloride; 10 mM phosphate buffer; 99.96% D2O
99.96% D2O
2 mM P4m RNA; 100 mM sodium chloride; 10 mM magnesium chloride; 10 mM phosphate buffer; 90% H2O, 10% D2O
90% H2O/10% D2O
2 mM P4m 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
3.84
Brunger
refinement
X-PLOR
2.84
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
U
7
n
7
U
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
1
A
A
O6
H41
G
C
1
27
1.60
minimized average
SOLUTION STRUCTURE OF THE RNASE P RNA (M1 RNA) P4 STEM C70U MUTANT 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
TYPE_28_PAIR
A
U
6
A
N3
U
6
1_555
A
G
22
A
O6
G
22
1_555
hydrog
TYPE_28_PAIR
A
U
6
A
O2
U
6
1_555
A
G
22
A
N1
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, C70U MUTANT, METAL BINDING SITE, RNA
1F6Z
PDB
1
1F6Z
1
27
1F6Z
1
27
1F6Z
A
1
1
27
1
P 1