List of data items in ./cif_bdlb13.0609
data_BDLB13.
_block.id BDLB13
loop_
_atom_site.id
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.cartn_x
_atom_site.cartn_y
_atom_site.cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.entity_id
_atom_site.entity_seq_num
1
O5*
C
A
1
.
19.172
33.767
25.153
1.00
8.82
1
1
2
C5*
C
A
1
.
20.547
33.724
24.631
1.00
8.64
1
1
3
C4*
C
A
1
.
20.798
32.272
24.362
1.00
8.98
1
1
4
O4*
C
A
1
.
19.761
31.476
25.121
1.00
8.98
1
1
5
C3*
C
A
1
.
20.738
31.734
22.953
1.00
9.18
1
1
122
C6M
+A
A
6
.
17.647
18.346
10.892
1.00
4.39
1
6
240
N1
G
A
12
.
14.338
18.628
-9.620
1.00
6.28
1
12
241
C2
G
A
12
.
15.645
18.286
-9.716
1.00
6.51
1
12
242
N2
G
A
12
.
15.983
17.106
-9.543
1.00
6.80
1
12
243
N3
G
A
12
.
16.715
19.042
-10.002
1.00
6.36
1
12
244
C4
G
A
12
.
16.314
20.314
-10.196
1.00
6.22
1
12
245
O5*
C
B
13
.
8.222
11.326
-8.855
1.00
15.65
1
1
246
C5*
C
B
13
.
9.373
10.642
-9.352
1.00
15.54
1
1
247
C4*
C
B
13
.
10.676
11.337
-9.066
1.00
14.87
1
1
248
O4*
C
B
13
.
10.581
12.738
-9.458
1.00
13.87
1
1
249
C3*
C
B
13
.
11.186
11.414
-7.645
1.00
14.83
1
1
367
C6M
+A
B
18
.
18.434
20.332
7.141
1.00
6.68
1
6
487
N2
G
B
24
.
19.173
25.089
26.511
1.00
2.22
1
12
488
N3
G
B
24
.
18.556
23.306
27.500
1.00
2.00
1
12
489
C4
G
B
24
.
17.489
22.773
28.126
1.00
2.00
1
12
490
O1
HOH
S
25
.
17.687
25.672
-10.801
1.00
10.02
2
.
491
O2
HOH
S
26
.
9.687
22.307
27.195
1.00
28.04
2
.
492
O3
HOH
S
27
.
5.605
18.820
13.966
1.00
30.80
2
.
493
O4
HOH
S
28
.
14.575
12.525
11.203
1.00
29.25
2
.
494
O5
HOH
S
29
.
1.095
3.844
28.581
1.00
14.94
2
.
_atom_sites.block_id BDLB13
_atom_sites.frac_tran_matrix[1][1] 0.039032
_atom_sites.frac_tran_matrix[1][2] 0.0
_atom_sites.frac_tran_matrix[1][3] 0.0
_atom_sites.frac_tran_matrix[2][1] 0.0
_atom_sites.frac_tran_matrix[2][2] 0.024759
_atom_sites.frac_tran_matrix[2][3] 0.0
_atom_sites.frac_tran_matrix[3][1] 0.0
_atom_sites.frac_tran_matrix[3][2] 0.0
_atom_sites.frac_tran_matrix[3][3] 0.014854
_cell.block_id BDLB13
_cell.length_a 25.620
_cell.length_b 40.390
_cell.length_c 67.320
_cell.angle_alpha 90.00
_cell.angle_beta 90.00
_cell.angle_gamma 90.00
loop_
_chem_comp.id
_chem_comp.name
_chem_comp.mon_nstd_flag
_chem_comp.mon_nstd_class
_chem_comp.mon_nstd_parent
A
ADE
no
.
.
T
THY
no
.
.
C
CYT
no
.
.
G
GUA
no
.
.
+A
METHYLADE
yes
'METHYLATED ADENINE'
ADE
HOH
WATER
.
.
.
loop_
_citation.id
_citation.title
_citation.country
_citation.journal_abbrev
_citation.journal_volume
_citation.page_first
_citation.year
_citation.page_last
_citation.journal_coden_ASTM
_citation.journal_coden_ISSN
primary
;
Methylation of the Ecori Recognition Site Does
not Alter DNA Conformation. The Crystal Structure
of d(CGCGAm6ATTCGCG) at 2.0 Angstroms Resolution
;
US
'J.Biol.Chem.'
263
17872
1988
17879
JBCHA3
0021-9258
loop_
_citation_author.citation_id
_citation_author.name
primary
'Frederick, C. A.'
primary
'Quigley, G. J.'
primary
'Van Der Marel, G. A.'
primary
'Van Boom, J. H.'
primary
'Wang, A. H. J.'
primary
'Rich, A.'
_computing.block_id BDLB13
_computing.structure_refinement 'NUCLSQ'
_diffrn.block_id BDLB13
_diffrn.ambient_temp 288.00
_diffrn_measurement.block_id BDLB13
_diffrn_measurement.device_type DIFFRACTOMETER
_diffrn_measurement.device_specific 'NICOLET'
_diffrn_radiation.block_id BDLB13
_diffrn_radiation.wavelength 1.54
loop_
_entity.id
_entity.type
_entity.src_method
1
polymer
'SYNTHETIC'
2
water
.
loop_
_entity_keywords.entity_id
_entity_keywords.text
1
'NUCLEIC ACID'
loop_
_entity_poly.entity_id
_entity_poly.nstd_monomer
_entity_poly.number_of_monomers
_entity_poly.type
1
yes
12
'polydeoxyribonucleotide'
loop_
_entity_poly_seq.entity_id
_entity_poly_seq.mon_id
_entity_poly_seq.num
1
C
1
1
G
2
1
C
3
1
G
4
1
A
5
1
+A
6
1
T
7
1
T
8
1
C
9
1
G
10
1
C
11
1
G
12
loop_
_exptl_crystal_grow_comp.id
_exptl_crystal_grow_comp.sol_id
_exptl_crystal_grow_comp.name
1
1
'MPD'
2
1
'Na Cacodylate'
3
1
'MgCl2'
4
1
'SPERMINE'
5
2
'MPD'
_struct.block_id BDLB13
_struct.title
;
5'-D(*CP*GP*CP*GP*AP*(M)AP*TP*TP*CP*GP*CP*G)-3'
;
_struct.keywords 'DEOXYRIBONUCLEIC ACID'
loop_
_struct_asym.id
_struct_asym.entity_id
_struct_asym.details
A
1
'NUCLEIC ACID'
B
1
'NUCLEIC ACID'
S
2
'H2O'
_struct_biol.id 1
_struct_biol.details 'FULL DUPLEX B DNA'
loop_
_struct_biol_gen.biol_id
_struct_biol_gen.asym_id
_struct_biol_gen.symmetry
1
A
1_555
1
B
1_555
1
S
1_555
loop_
_struct_biol_keywords.biol_id
_struct_biol_keywords.text
1
'DNA'
1
'B DNA'
1
'DNA DUPLEX'
1
'METHYLATED ADENINE'
1
'MODIFIED ADENINE'
loop_
_struct_conf.id
_struct_conf.conf_type_id
_struct_conf.beg_label_comp_id
_struct_conf.beg_label_asym_id
_struct_conf.beg_label_seq_id
_struct_conf.end_label_comp_id
_struct_conf.end_label_asym_id
_struct_conf.end_label_seq_id
CHAIN-A
HELX-RHB
C
A
1
G
A
12
CHAIN-B
HELX-RHB
C
B
13
G
B
24
loop_
_struct_conf_type.id
_struct_conf_type.criteria
HELX-RHB
'AUTHOR JUDGEMENT'
loop_
_struct_conn_type.id
_struct_conn_type.criteria
hydrog
;
N - O distance > 2.5 Angstoms and < 3.5 Angstroms
N - O - C angle < 120 degrees
;
covale
'AUTHOR JUDGEMENT'
loop_
_struct_conn.id
_struct_conn.conn_type_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_symmetry
_struct_conn.details
1
hydrog
C
A
1
O2
1_555
G
B
24
N2
1_555
WATSON-CRICK
2
hydrog
C
A
1
N3
1_555
G
B
24
N1
1_555
WATSON-CRICK
3
hydrog
C
A
1
N4
1_555
G
B
24
O6
1_555
WATSON-CRICK
4
hydrog
G
A
2
N2
1_555
C
B
23
O2
1_555
WATSON-CRICK
5
hydrog
G
A
2
N1
1_555
C
B
23
N3
1_555
WATSON-CRICK
6
hydrog
G
A
2
O6
1_555
C
B
23
N4
1_555
WATSON-CRICK
7
hydrog
C
A
3
O2
1_555
G
B
22
N2
1_555
WATSON-CRICK
8
hydrog
C
A
3
N3
1_555
G
B
22
N1
1_555
WATSON-CRICK
9
hydrog
C
A
3
N4
1_555
G
B
22
O6
1_555
WATSON-CRICK
10
hydrog
G
A
4
N2
1_555
C
B
21
O2
1_555
WATSON-CRICK
11
hydrog
G
A
4
N1
1_555
C
B
21
N3
1_555
WATSON-CRICK
12
hydrog
G
A
4
O6
1_555
C
B
21
N4
1_555
WATSON-CRICK
13
hydrog
A
A
5
N1
1_555
T
B
20
N3
1_555
WATSON-CRICK
14
hydrog
A
A
5
N6
1_555
T
B
20
O4
1_555
WATSON-CRICK
15
hydrog
+A
A
6
N1
1_555
T
B
19
N3
1_555
WATSON-CRICK
16
hydrog
+A
A
6
N6
1_555
T
B
19
O4
1_555
WATSON-CRICK
17
hydrog
T
A
7
N3
1_555
+A
B
18
N1
1_555
WATSON-CRICK
18
hydrog
T
A
7
O4
1_555
+A
B
18
N6
1_555
WATSON-CRICK
19
hydrog
T
A
8
N3
1_555
A
B
17
N1
1_555
WATSON-CRICK
20
hydrog
T
A
8
O4
1_555
A
B
17
N6
1_555
WATSON-CRICK
21
hydrog
C
A
9
O2
1_555
G
B
16
N2
1_555
WATSON-CRICK
22
hydrog
C
A
9
N3
1_555
G
B
16
N1
1_555
WATSON-CRICK
23
hydrog
C
A
9
N4
1_555
G
B
16
O6
1_555
WATSON-CRICK
24
hydrog
G
A
10
N2
1_555
C
B
15
O2
1_555
WATSON-CRICK
25
hydrog
G
A
10
N1
1_555
C
B
15
N3
1_555
WATSON-CRICK
26
hydrog
G
A
10
O6
1_555
C
B
15
N4
1_555
WATSON-CRICK
27
hydrog
C
A
11
O2
1_555
G
B
14
N2
1_555
WATSON-CRICK
28
hydrog
C
A
11
N3
1_555
G
B
14
N1
1_555
WATSON-CRICK
29
hydrog
C
A
11
N4
1_555
G
B
14
O6
1_555
WATSON-CRICK
30
hydrog
G
A
12
N2
1_555
C
B
13
O2
1_555
WATSON-CRICK
31
hydrog
G
A
12
N1
1_555
C
B
13
N3
1_555
WATSON-CRICK
32
hydrog
G
A
12
O6
1_555
C
B
13
N4
1_555
WATSON-CRICK
33
covale
+A
A
6
N6
1_555
+A
A
6
C6M
1_555
'MODIFIER COVALENT LINK'
34
covale
+A
B
18
N6
1_555
+A
B
18
C6M
1_555
'MODIFIER COVALENT LINK'
_symmetry.block_id BDLB13
_symmetry.space_group_name_H-M 'P 21 21 21'