0.024643
0.014227
0.000000
0.000000
0.028455
0.000000
0.000000
0.000000
0.017811
0.00000
0.00000
0.00000
Kiliszek, A.
Kierzek, R.
Krzyzosiak, W.J.
Rypniewski, W.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
18
90.00
90.00
120.00
40.580
40.580
56.144
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
H2 O
18.015
WATER
non-polymer
N
1
N
O
N
2
N
P
N
3
N
O
N
4
N
O
N
5
N
O
N
6
N
C
N
7
R
C
N
8
N
O
N
9
S
C
N
10
N
O
N
11
R
C
N
12
N
O
N
13
R
C
N
14
N
N
N
15
N
C
N
16
N
O
N
17
N
N
N
18
N
C
N
19
N
N
N
20
N
C
N
21
N
C
N
22
N
H
N
23
N
H
N
24
N
H
N
25
N
H
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
O
N
37
N
P
N
38
N
O
N
39
N
O
N
40
N
O
N
41
N
C
N
42
R
C
N
43
N
O
N
44
S
C
N
45
N
O
N
46
R
C
N
47
N
O
N
48
R
C
Y
49
N
N
Y
50
N
C
Y
51
N
N
Y
52
N
C
N
53
N
C
N
54
N
O
N
55
N
N
N
56
N
C
N
57
N
N
N
58
N
N
Y
59
N
C
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
N
64
N
H
N
65
N
H
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
O
N
75
N
H
N
76
N
H
N
1
N
sing
N
2
N
sing
N
3
N
doub
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
sing
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
doub
N
28
N
sing
N
29
N
doub
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
sing
N
34
N
doub
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
doub
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
Y
61
N
sing
Y
62
N
sing
Y
63
N
doub
N
64
N
sing
Y
65
N
sing
N
66
N
sing
Y
67
N
doub
N
68
N
doub
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
doub
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
sing
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
40
8155
8162
10.1093/nar/gks557
22718980
Crystallographic characterization of CCG repeats.
2012
10.2210/pdb4e59/pdb
pdb_00004e59
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
CCD
2010-10-05
MARMOSAIC 225 mm CCD
Si
SINGLE WAVELENGTH
M
x-ray
1
0.9184
1.0
14.2
BESSY
0.9184
SYNCHROTRON
BESSY BEAMLINE 14.2
2516.569
RNA duplex containing CCG repeats
2
syn
polymer
18.015
water
16
nat
water
no
no
GCCGCCGC
GCCGCCGC
A,B
polyribonucleotide
n
n
n
n
n
n
n
n
1
1.77
30.41
VAPOR DIFFUSION, HANGING DROP
5.6
magnesium acetate, MES and ammonium sulphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 303K
303
-3.491
1
19
A
1
B
5
-2.878
A_G1:C5_B
1
-14.140
-0.420
0.172
-0.453
-2.460
1
19
A
2
B
4
-3.431
A_C2:G4_B
2
-11.623
0.051
-0.093
-0.338
2.220
1
19
A
4
B
2
3.313
A_G4:C2_B
3
-9.655
-0.433
0.137
-0.129
3.252
1
19
A
5
B
1
-0.697
A_C5:G1_B
4
-14.000
0.270
-0.076
-0.268
3.066
37.871
A
A
1
2
5.707
B
B
5
4
3.249
3.697
-0.155
-1.685
AA_G1C2:G4C5_BB
1
1.778
-2.745
37.656
-3.056
0.460
4.828
64.742
A
A
2
4
19.359
B
B
4
2
6.047
20.444
-0.300
-3.425
AA_C2G4:C2G4_BB
2
-1.528
1.447
61.748
-4.673
0.170
2.877
35.340
A
A
4
5
12.653
B
B
2
1
3.244
7.619
0.217
-1.445
AA_G4C5:G1C2_BB
3
2.344
-3.892
34.457
-3.447
-0.029
pdbx_entity_src_syn
software
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
repository
Initial release
Refinement description
Source and taxonomy
Data collection
Database references
Refinement description
1
0
2012-12-12
1
1
2017-11-15
1
2
2023-09-13
_pdbx_entity_src_syn.ncbi_taxonomy_id
_pdbx_entity_src_syn.organism_scientific
_software.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
Similar sequence but with an LNA nucleotide
RCSB
Y
RCSB
2012-03-14
REL
REL
HOH
water
This sequence is a part of mRNA in humans
9606
Homo sapiens
sample
4E58
PDB
experimental model
HOH
8
2
HOH
HOH
101
A
HOH
10
2
HOH
HOH
102
A
HOH
11
2
HOH
HOH
103
A
HOH
12
2
HOH
HOH
104
A
HOH
18
2
HOH
HOH
105
A
HOH
19
2
HOH
HOH
106
A
HOH
21
2
HOH
HOH
107
A
HOH
22
2
HOH
HOH
108
A
HOH
23
2
HOH
HOH
109
A
HOH
1
2
HOH
HOH
101
B
HOH
2
2
HOH
HOH
102
B
HOH
3
2
HOH
HOH
103
B
HOH
6
2
HOH
HOH
104
B
HOH
9
2
HOH
HOH
105
B
HOH
13
2
HOH
HOH
106
B
HOH
14
2
HOH
HOH
107
B
G
1
n
1
G
1
A
C
2
n
2
C
2
A
C
3
n
3
C
3
A
G
4
n
4
G
4
A
C
5
n
5
C
5
A
C
6
n
6
C
6
A
G
7
n
7
G
7
A
C
8
n
8
C
8
A
G
1
n
1
G
1
B
C
2
n
2
C
2
B
C
3
n
3
C
3
B
G
4
n
4
G
4
B
C
5
n
5
C
5
B
C
6
n
6
C
6
B
G
7
n
7
G
7
B
C
8
n
8
C
8
B
author_and_software_defined_assembly
PISA
2
dimeric
software_defined_assembly
PISA
6
hexameric
570
-4
3060
3640
-46
7280
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
-0.5000000000
-0.8660254038
0.0000000000
0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
2_555
-y,x-y,z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
-0.5000000000
0.8660254038
0.0000000000
-0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
3_555
-x+y,-x,z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
1
A
HOH
105
C
HOH
1
A
HOH
106
C
HOH
1
B
HOH
105
D
HOH
1
B
HOH
106
D
HOH
1
A
C5'
C
8
A
C5'
C
8
1
Y
1
A
C4'
C
8
A
C4'
C
8
1
Y
1
A
O4'
C
8
A
O4'
C
8
1
Y
1
A
C3'
C
8
A
C3'
C
8
1
Y
1
A
O3'
C
8
A
O3'
C
8
1
Y
1
A
C2'
C
8
A
C2'
C
8
1
Y
1
A
O2'
C
8
A
O2'
C
8
1
Y
1
A
C1'
C
8
A
C1'
C
8
1
Y
1
A
N1
C
8
A
N1
C
8
1
Y
1
A
C2
C
8
A
C2
C
8
1
Y
1
A
O2
C
8
A
O2
C
8
1
Y
1
A
N3
C
8
A
N3
C
8
1
Y
1
A
C4
C
8
A
C4
C
8
1
Y
1
A
N4
C
8
A
N4
C
8
1
Y
1
A
C5
C
8
A
C5
C
8
1
Y
1
A
C6
C
8
A
C6
C
8
1
Y
1
B
C5'
C
8
B
C5'
C
8
1
Y
1
B
C4'
C
8
B
C4'
C
8
1
Y
1
B
O4'
C
8
B
O4'
C
8
1
Y
1
B
C3'
C
8
B
C3'
C
8
1
Y
1
B
O3'
C
8
B
O3'
C
8
1
Y
1
B
C2'
C
8
B
C2'
C
8
1
Y
1
B
O2'
C
8
B
O2'
C
8
1
Y
1
B
C1'
C
8
B
C1'
C
8
1
Y
1
B
N1
C
8
B
N1
C
8
1
Y
1
B
C2
C
8
B
C2
C
8
1
Y
1
B
O2
C
8
B
O2
C
8
1
Y
1
B
N3
C
8
B
N3
C
8
1
Y
1
B
C4
C
8
B
C4
C
8
1
Y
1
B
N4
C
8
B
N4
C
8
1
Y
1
B
C5
C
8
B
C5
C
8
1
Y
1
B
C6
C
8
B
C6
C
8
1
Y
1
-3.71
0.40
120.30
116.59
A
A
A
C6
N1
C2
C
C
C
6
6
6
N
1
-4.29
0.70
121.90
117.61
A
A
A
N3
C2
O2
C
C
C
6
6
6
N
27.79
4.8628
0.0000
-0.0000
4.8628
-0.0000
-9.7256
0.3035
0.2553
0.2570
0.2553
1.540
18.715
501
5073
5073
100.00
99.41
0.25
RANDOM
1
THROUGHOUT
1.99
MOLECULAR REPLACEMENT
30.22
0.16
0.50
4E58
ML
FLAT BULK SOLVENT MODEL
63.918
0.458
1.540
18.715
16
316
0
300
0
0.010
332
1.290
516
13.993
164
0.076
70
0.015
14
0.3627
0.3411
1.6950
130
161
1270
100.00
1.54
20.00
4E59
5101
5101
0
0
0.040
1
26.14
4.3
99.9
1.54
1.57
2.06
262
0.711
1
3.8
100.0
data collection
MAR345
phasing
PHASER
refinement
PHENIX
(phenix.refine: 1.7_650)
data reduction
HKL-2000
data scaling
HKL-2000
Crystal structure of GCCGCCGC duplex
1
N
N
1
N
N
2
N
N
2
N
N
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
B
C
5
B
N3
C
5
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
B
C
5
B
O2
C
5
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
B
C
5
B
N4
C
5
1_555
hydrog
WATSON-CRICK
A
C
2
A
N3
C
2
1_555
B
G
4
B
N1
G
4
1_555
hydrog
WATSON-CRICK
A
C
2
A
N4
C
2
1_555
B
G
4
B
O6
G
4
1_555
hydrog
WATSON-CRICK
A
C
2
A
O2
C
2
1_555
B
G
4
B
N2
G
4
1_555
hydrog
WATSON-CRICK
A
G
4
A
N1
G
4
1_555
B
C
2
B
N3
C
2
1_555
hydrog
WATSON-CRICK
A
G
4
A
N2
G
4
1_555
B
C
2
B
O2
C
2
1_555
hydrog
WATSON-CRICK
A
G
4
A
O6
G
4
1_555
B
C
2
B
N4
C
2
1_555
hydrog
WATSON-CRICK
A
C
5
A
N3
C
5
1_555
B
G
1
B
N1
G
1
1_555
hydrog
WATSON-CRICK
A
C
5
A
N4
C
5
1_555
B
G
1
B
O6
G
1
1_555
hydrog
WATSON-CRICK
A
C
5
A
O2
C
5
1_555
B
G
1
B
N2
G
1
1_555
RNA
3' slippery duplexes, X-linked mental retardation, Huntington's disease, myotonic dystrophy type 1, RNA, CCG repeats
4E59
PDB
1
1
4E59
GCCGCCGC
1
8
4E59
1
8
4E59
A
1
1
8
1
8
4E59
1
8
4E59
B
1
1
8
146
H 3