1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Motackova, V.
Sanderova, H.
Zidek, L.
Novacek, J.
Padrta, P.
Svenkova, A.
Jonak, J.
Krasny, L.
Sklenar, V.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
US
Proteins
PSFGEY
0867
0887-3585
78
1807
1810
10.1002/prot.22708
20310067
Solution structure of the N-terminal domain of Bacillus subtilis delta subunit of RNA polymerase and its classification based on structural homologs
2010
10.2210/pdb2krc/pdb
pdb_00002krc
11769.083
DNA-directed RNA polymerase subunit delta
residues 2-92
1
man
polymer
N delta, RNAP delta factor
no
no
GIKQYSQEELKEMALVEIAHELFEEHKKPVPFQELLNEIASLLGVKKEELGDRIAQFYTDLNIDGRFLALSDQTWGLRSW
YPYDQLDEETQLEHHHHHH
GIKQYSQEELKEMALVEIAHELFEEHKKPVPFQELLNEIASLLGVKKEELGDRIAQFYTDLNIDGRFLALSDQTWGLRSW
YPYDQLDEETQLEHHHHHH
A
polypeptide(L)
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
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
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
sample
1423
Bacillus subtilis
469008
Escherichia coli
BL21(DE3)
pET22b
vector
database_2
pdbx_nmr_software
pdbx_nmr_spectrometer
pdbx_struct_assembly
pdbx_struct_oper_list
struct_ref_seq_dif
repository
Initial release
Version format compliance
Data collection
Database references
Derived calculations
1
0
2010-04-07
1
1
2011-07-13
1
2
2022-03-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_pdbx_nmr_spectrometer.model
_struct_ref_seq_dif.details
BMRB
Y
PDBJ
2009-12-16
REL
REL
2341
734
544
564
499
0
0
66
66
structures with the lowest energy
100
10
1
2D 1H-15N HSQC
2D 1H-13C HMQC
3D CBCA(CO)NH
3D HNCACB
3D HNCA
3D HN(CO)CA
3D HNCO
3D HNHA
3D HCCH-TOCSY
3D 1H-15N NOESY
3D 1H-13C NOESY
(HB)CB(CGCD)HD
2D 1H-15N IPAP
2D HN[C]-S3E
2D (H)CACO-IPAP
2D 13C-coupled 1H-13C HSQC
2D 1H-15N IPAP
2D HN[C]-S3E
2D (H)CACO-IPAP
2D 13C-coupled 1H-13C HSQC
2D 13C-detected CON
2D 13C-detected CON
2D 1H-15N IPAP
2D HN[C]-S3E
2D (H)CACO-IPAP
2D 13C-coupled 1H-13C HSQC
10
mM
50
uM
20
mM
10
mM
50
uM
20
mM
14.29
mg/mL
10
mM
50
uM
20
mM
5
%
10
6.6
1
atm
301
K
molecular dynamics, simulated annealing
1
lowest energy
10 mM sodium chloride-1, 50 uM sodium azide-2, 20 mM phosphate buffer-3, 90% H2O/10% D2O
90% H2O/10% D2O
10 mM sodium chloride-4, 50 uM sodium azide-5, 20 mM phosphate buffer-6, 14.29 mg/mL filamentous Pf1 bacteriophage-7, 90% H2O/10% D2O
90% H2O/10% D2O
10 mM sodium chloride-8, 50 uM sodium azide-9, 20 mM phosphate buffer-10, 5 % polyacrylamide gel-11, 90% H2O/10% D2O
90% H2O/10% D2O
Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
processing
NMRPipe
3.0
Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
processing
NMRDraw
3.0
Goddard
chemical shift assignment
Sparky
3.111
Goddard
peak picking
Sparky
3.111
Linge, O'Donoghue and Nilges
noe assignment
ARIA
2.1
Brunger, Adams, Clore, Gros, Nilges and Read
structure solution
CNS
1.2
Brunger, Adams, Clore, Gros, Nilges and Read
refinement
CNS
1.2
Brunger
refinement
X-PLOR
Petr Novak
dipolar coupling determination
S3EPY
Petr Novak
peak picking
S3EPY
600
Bruker
AVANCE
Bruker Avance
GLY
2
n
1
GLY
2
A
ILE
3
n
2
ILE
3
A
LYS
4
n
3
LYS
4
A
GLN
5
n
4
GLN
5
A
TYR
6
n
5
TYR
6
A
SER
7
n
6
SER
7
A
GLN
8
n
7
GLN
8
A
GLU
9
n
8
GLU
9
A
GLU
10
n
9
GLU
10
A
LEU
11
n
10
LEU
11
A
LYS
12
n
11
LYS
12
A
GLU
13
n
12
GLU
13
A
MET
14
n
13
MET
14
A
ALA
15
n
14
ALA
15
A
LEU
16
n
15
LEU
16
A
VAL
17
n
16
VAL
17
A
GLU
18
n
17
GLU
18
A
ILE
19
n
18
ILE
19
A
ALA
20
n
19
ALA
20
A
HIS
21
n
20
HIS
21
A
GLU
22
n
21
GLU
22
A
LEU
23
n
22
LEU
23
A
PHE
24
n
23
PHE
24
A
GLU
25
n
24
GLU
25
A
GLU
26
n
25
GLU
26
A
HIS
27
n
26
HIS
27
A
LYS
28
n
27
LYS
28
A
LYS
29
n
28
LYS
29
A
PRO
30
n
29
PRO
30
A
VAL
31
n
30
VAL
31
A
PRO
32
n
31
PRO
32
A
PHE
33
n
32
PHE
33
A
GLN
34
n
33
GLN
34
A
GLU
35
n
34
GLU
35
A
LEU
36
n
35
LEU
36
A
LEU
37
n
36
LEU
37
A
ASN
38
n
37
ASN
38
A
GLU
39
n
38
GLU
39
A
ILE
40
n
39
ILE
40
A
ALA
41
n
40
ALA
41
A
SER
42
n
41
SER
42
A
LEU
43
n
42
LEU
43
A
LEU
44
n
43
LEU
44
A
GLY
45
n
44
GLY
45
A
VAL
46
n
45
VAL
46
A
LYS
47
n
46
LYS
47
A
LYS
48
n
47
LYS
48
A
GLU
49
n
48
GLU
49
A
GLU
50
n
49
GLU
50
A
LEU
51
n
50
LEU
51
A
GLY
52
n
51
GLY
52
A
ASP
53
n
52
ASP
53
A
ARG
54
n
53
ARG
54
A
ILE
55
n
54
ILE
55
A
ALA
56
n
55
ALA
56
A
GLN
57
n
56
GLN
57
A
PHE
58
n
57
PHE
58
A
TYR
59
n
58
TYR
59
A
THR
60
n
59
THR
60
A
ASP
61
n
60
ASP
61
A
LEU
62
n
61
LEU
62
A
ASN
63
n
62
ASN
63
A
ILE
64
n
63
ILE
64
A
ASP
65
n
64
ASP
65
A
GLY
66
n
65
GLY
66
A
ARG
67
n
66
ARG
67
A
PHE
68
n
67
PHE
68
A
LEU
69
n
68
LEU
69
A
ALA
70
n
69
ALA
70
A
LEU
71
n
70
LEU
71
A
SER
72
n
71
SER
72
A
ASP
73
n
72
ASP
73
A
GLN
74
n
73
GLN
74
A
THR
75
n
74
THR
75
A
TRP
76
n
75
TRP
76
A
GLY
77
n
76
GLY
77
A
LEU
78
n
77
LEU
78
A
ARG
79
n
78
ARG
79
A
SER
80
n
79
SER
80
A
TRP
81
n
80
TRP
81
A
TYR
82
n
81
TYR
82
A
PRO
83
n
82
PRO
83
A
TYR
84
n
83
TYR
84
A
ASP
85
n
84
ASP
85
A
GLN
86
n
85
GLN
86
A
LEU
87
n
86
LEU
87
A
ASP
88
n
87
ASP
88
A
GLU
89
n
88
GLU
89
A
GLU
90
n
89
GLU
90
A
THR
91
n
90
THR
91
A
GLN
92
n
91
GLN
92
A
LEU
93
n
92
LEU
93
A
GLU
94
n
93
GLU
94
A
HIS
95
n
94
HIS
95
A
HIS
96
n
95
HIS
96
A
HIS
97
n
96
HIS
97
A
HIS
98
n
97
HIS
98
A
HIS
99
n
98
HIS
99
A
HIS
100
n
99
HIS
100
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
A
N
VAL
31
A
N
VAL
30
A
O
TRP
76
A
O
TRP
75
A
O
GLY
77
A
O
GLY
76
A
N
LEU
69
A
N
LEU
68
9
A
CA
GLN
92
PLANAR
1
A
A
HH21
OE1
ARG
GLU
67
94
1.58
1
A
A
HD1
OE1
HIS
GLU
21
22
1.59
2
A
A
OE1
HD1
GLU
HIS
25
95
1.57
2
A
A
OE2
HZ1
GLU
LYS
25
28
1.57
2
A
A
HZ1
OE2
LYS
GLU
12
13
1.59
3
A
A
OE1
HZ3
GLU
LYS
25
28
1.57
3
A
A
HE2
OE1
HIS
GLU
21
89
1.58
3
A
A
HG
OE2
SER
GLU
80
89
1.59
3
A
A
HE2
OE1
HIS
GLU
27
39
1.59
4
A
A
HE2
OE2
HIS
GLU
27
39
1.59
4
A
A
HZ2
OE1
LYS
GLU
47
50
1.59
7
A
A
HZ2
OE1
LYS
GLU
4
25
1.58
7
A
A
HE2
OE1
HIS
GLU
27
39
1.59
8
A
A
HD1
OE2
HIS
GLU
21
22
1.56
8
A
A
OD2
HD1
ASP
HIS
85
98
1.58
8
A
A
HZ3
OE2
LYS
GLU
48
49
1.59
9
A
A
HZ1
OE1
LYS
GLU
4
25
1.58
10
A
A
H1
OE1
GLY
GLU
2
90
1.60
2
A
ARG
79
0.092
SIDE CHAIN
4
A
ARG
67
0.108
SIDE CHAIN
1
A
ILE
3
63.72
-96.28
1
A
GLN
5
-161.20
21.65
1
A
PHE
68
62.35
146.27
1
A
LEU
71
-78.06
-84.40
1
A
SER
72
-90.80
-61.32
1
A
ASP
73
-162.03
-61.57
1
A
TYR
84
177.82
-70.27
1
A
ASP
85
-147.19
10.75
1
A
GLN
86
-173.48
117.66
1
A
LEU
93
61.38
89.24
1
A
GLU
94
49.77
105.16
1
A
HIS
97
52.45
74.17
1
A
HIS
99
-156.94
-55.89
2
A
LYS
4
-68.03
1.73
2
A
LEU
71
-76.45
-83.24
2
A
ASP
73
-153.35
-52.68
2
A
ARG
79
-63.80
0.16
2
A
GLU
90
-75.90
21.70
2
A
GLN
92
-126.25
-64.63
2
A
LEU
93
-144.14
-153.11
2
A
HIS
97
70.40
-70.93
2
A
HIS
98
-162.26
42.26
2
A
HIS
99
78.91
-48.00
3
A
ARG
67
-101.18
-157.03
3
A
PHE
68
48.80
107.90
3
A
LEU
71
-98.53
-90.12
3
A
SER
72
-91.38
-61.52
3
A
GLN
74
68.87
-12.03
3
A
TYR
84
175.70
77.35
3
A
ASP
85
64.60
-63.36
3
A
GLN
86
-91.09
-70.23
3
A
LEU
87
71.29
98.40
3
A
ASP
88
76.12
80.42
3
A
LEU
93
82.17
83.20
3
A
GLU
94
59.52
131.24
3
A
HIS
97
67.00
-81.00
3
A
HIS
98
163.73
-178.04
4
A
LYS
4
-65.39
15.36
4
A
LEU
71
-76.75
-91.05
4
A
SER
72
-92.40
-60.34
4
A
ASP
73
-157.44
-37.85
4
A
TYR
84
-179.40
84.42
4
A
ASP
85
70.81
-40.70
4
A
GLN
92
-126.06
-62.91
4
A
LEU
93
-167.94
-145.30
4
A
GLU
94
-68.37
69.16
4
A
HIS
97
56.01
-82.17
5
A
ILE
3
-135.80
-82.75
5
A
GLN
5
-158.80
20.16
5
A
LEU
71
-78.93
-80.93
5
A
ASP
73
-164.78
-40.45
5
A
ARG
79
-75.17
21.52
5
A
TYR
84
-169.36
-85.41
5
A
ASP
85
-151.29
-18.05
5
A
LEU
87
-162.64
93.23
5
A
LEU
93
73.04
68.31
5
A
GLU
94
65.22
126.88
5
A
HIS
97
61.57
76.20
6
A
ILE
3
-131.95
-83.07
6
A
GLN
5
-150.85
18.82
6
A
LEU
71
-82.34
-89.39
6
A
ASP
73
-172.60
-36.77
6
A
TYR
84
-179.40
-156.60
6
A
GLU
89
175.18
155.66
6
A
GLN
92
-122.97
-63.14
6
A
LEU
93
85.40
64.66
6
A
GLU
94
71.44
139.17
6
A
HIS
99
69.93
165.70
7
A
ILE
3
-138.82
-82.96
7
A
GLN
5
-149.13
16.25
7
A
LEU
71
-77.95
-87.84
7
A
SER
72
-97.43
-60.23
7
A
ASP
73
-149.77
-42.06
7
A
TYR
84
-172.10
-162.33
7
A
LEU
93
85.57
94.25
7
A
GLU
94
59.31
-33.21
7
A
HIS
96
-39.59
-19.65
7
A
HIS
99
176.54
-51.03
8
A
ILE
3
63.17
-102.36
8
A
GLN
5
-158.62
22.11
8
A
ILE
64
-101.27
59.51
8
A
LEU
71
-79.84
-88.34
8
A
SER
72
-96.34
-60.02
8
A
ASP
73
-155.08
-70.83
8
A
TYR
84
-172.02
29.19
8
A
ASP
85
80.76
173.71
8
A
GLN
86
67.56
-60.77
8
A
GLU
90
-67.11
21.17
8
A
GLN
92
-126.22
-57.07
8
A
LEU
93
62.22
85.89
8
A
GLU
94
50.13
79.01
8
A
HIS
98
-178.15
-41.63
9
A
ILE
3
58.81
-93.60
9
A
GLN
5
-175.68
22.80
9
A
ILE
64
-102.09
65.57
9
A
ASP
65
-122.23
-62.85
9
A
LEU
71
-103.40
-81.15
9
A
SER
72
-94.18
35.79
9
A
ASP
73
80.19
-53.08
9
A
SER
80
-69.46
2.41
9
A
TYR
84
-159.98
64.90
9
A
ASP
85
71.74
-49.78
9
A
ASP
88
59.52
10.74
9
A
GLU
94
58.26
-78.78
9
A
HIS
96
-40.12
2.53
9
A
HIS
97
-173.15
-72.71
9
A
HIS
98
59.61
-80.33
9
A
HIS
99
62.15
113.05
10
A
ILE
64
-100.25
68.93
10
A
ASP
65
-127.34
-76.18
10
A
LEU
71
-76.40
-82.35
10
A
SER
72
-95.22
-60.63
10
A
ASP
73
-153.67
-57.31
10
A
TYR
84
-171.56
-169.57
10
A
GLU
90
-68.24
21.15
10
A
GLN
92
-129.29
-59.35
10
A
LEU
93
79.78
74.05
10
A
GLU
94
59.61
105.84
10
A
HIS
95
-45.19
101.68
10
A
HIS
98
-79.75
-85.28
lowest energy, model 1
Solution structure of the N-terminal domain of Bacillus subtilis delta subunit of RNA polymerase
1
N
N
A
SER
7
A
SER
6
HELX_P
A
GLU
13
A
GLU
12
1
1
7
A
ALA
15
A
ALA
14
HELX_P
A
LYS
28
A
LYS
27
1
2
14
A
PHE
33
A
PHE
32
HELX_P
A
GLY
45
A
GLY
44
1
3
13
A
LYS
47
A
LYS
46
HELX_P
A
LEU
51
A
LEU
50
5
4
5
A
GLY
52
A
GLY
51
HELX_P
A
ILE
64
A
ILE
63
1
5
13
A
LEU
78
A
LEU
77
HELX_P
A
TYR
82
A
TYR
81
5
6
5
TRANSCRIPTION
RNA polymerase, delta subunit, gram-positive bacteria, DNA-directed RNA polymerase, Nucleotidyltransferase, Transcription, Transferase
RPOE_BACSU
UNP
1
2
P12464
GIKQYSQEELKEMALVEIAHELFEEHKKPVPFQELLNEIASLLGVKKEELGDRIAQFYTDLNIDGRFLALSDQTWGLRSW
YPYDQLDEETQ
2
92
2KRC
2
92
P12464
A
1
1
91
1
expression tag
LEU
93
2KRC
A
P12464
UNP
92
1
expression tag
GLU
94
2KRC
A
P12464
UNP
93
1
expression tag
HIS
95
2KRC
A
P12464
UNP
94
1
expression tag
HIS
96
2KRC
A
P12464
UNP
95
1
expression tag
HIS
97
2KRC
A
P12464
UNP
96
1
expression tag
HIS
98
2KRC
A
P12464
UNP
97
1
expression tag
HIS
99
2KRC
A
P12464
UNP
98
1
expression tag
HIS
100
2KRC
A
P12464
UNP
99
3
anti-parallel
anti-parallel
A
VAL
31
A
VAL
30
A
PRO
32
A
PRO
31
A
THR
75
A
THR
74
A
GLY
77
A
GLY
76
A
LEU
69
A
LEU
68
A
ALA
70
A
ALA
69