1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Mackereth, C.D.
Arrowsmith, C.H.
Edwards, A.M.
Mcintosh, L.P.
Northeast Structural Genomics Consortium (NESG)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
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
C3 H7 N O2 S
121.158
y
CYSTEINE
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
Zn 2
65.409
ZINC ION
non-polymer
US
Proc.Natl.Acad.Sci.USA
PNASA6
0040
0027-8424
97
6316
6321
10.1073/pnas.97.12.6316
10841539
Zinc-bundle structure of the essential RNA polymerase subunit RPB10 from Methanobacterium thermoautotrophicum.
2000
10.2210/pdb1ef4/pdb
pdb_00001ef4
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
6444.494
DNA-DIRECTED RNA POLYMERASE
2.7.7.6
SUBUNIT RPB10
1
man
polymer
65.409
ZINC ION
1
syn
non-polymer
SUBUNIT N
no
no
MIPVRCLSCGKPVSAYFNEYQRRVADGEDPKDVLDDLGLKRYCCRRMLISHVETW
MIPVRCLSCGKPVSAYFNEYQRRVADGEDPKDVLDDLGLKRYCCRRMLISHVETW
A
TT11
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
Methanothermobacter
Escherichia
sample
145262
Methanothermobacter thermautotrophicus
562
Escherichia coli
PLASMID
PET15B
Northeast Structural Genomics Consortium
NESG
PSI, Protein Structure Initiative
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_conn_angle
pdbx_struct_oper_list
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2000-06-14
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
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Y
RCSB
Y
RCSB
2000-02-07
REL
REL
ZN
ZINC ION
THIS STRUCTURE WAS DETERMINED USING TRIPLE- RESONANCE NMR SPECTROSCOPY.
structures with acceptable covalent geometry
60
20
3D METHYL-METHYL 13C_ SEPARATED NOESY
2D NOESY
3D_13C-SEPARATED_ NOESY
3D_15N-SEPARATED_ NOESY
HNHA
2D CT-HMQC-J
150mM_NACL
7.50
AMBIENT
303.00
K
REFINED USING ARIA AMBIGUOUS AND UNAMBIGUOUS RESTRAINTS, AND INCLUDING RESTRAINTS FOR DIHEDRAL ANGLES AND HYDROGEN BOND DISTANCES. ZINC COORDINATION TO CYS 6,9,43,44 WITH IDEALIZED TETRAHEDRAL RESTRAINTS WERE ADDED IN THE FINAL ROUNDS OF REFINEMENT; THE COORDINATING LIGANDS AND THEIR GEOMETRIC ARRANGEMENT WERE IDENTIFIED BASED ON INITIAL NOE-DERIVED STRUCTURES CALCULATED WITHOUT INCLUSION OF THE METAL ION. THREE N- TERMINAL RESIDUES (GLY-SER-HIS) REMAINING FROM CLEAVAGE OF THE HIS-TAG WERE DISORDERED AND NOT INCLUDED IN THE FINAL ENSEMBLE.
DISTANCE GEOMETRY WITH SIMULATED ANNEALING
1
0.5MM RPB10 U-15N,13C 20MM DEUTERATED D-TRIS; 0.15M NACL; 2MM BETA- MERCAPTOETHANOL; 99% D2O, 1% H2O
BRUNGER (X-PLOR), NILGES (ARIA)
refinement
X-PLOR 3.851, ARIA
1999
structure solution
VNMR
6
structure solution
Felix
95.0
500
Varian
UNITY
ZN
56
2
ZN
ZN
56
A
MET
1
n
1
MET
1
A
ILE
2
n
2
ILE
2
A
PRO
3
n
3
PRO
3
A
VAL
4
n
4
VAL
4
A
ARG
5
n
5
ARG
5
A
CYS
6
n
6
CYS
6
A
LEU
7
n
7
LEU
7
A
SER
8
n
8
SER
8
A
CYS
9
n
9
CYS
9
A
GLY
10
n
10
GLY
10
A
LYS
11
n
11
LYS
11
A
PRO
12
n
12
PRO
12
A
VAL
13
n
13
VAL
13
A
SER
14
n
14
SER
14
A
ALA
15
n
15
ALA
15
A
TYR
16
n
16
TYR
16
A
PHE
17
n
17
PHE
17
A
ASN
18
n
18
ASN
18
A
GLU
19
n
19
GLU
19
A
TYR
20
n
20
TYR
20
A
GLN
21
n
21
GLN
21
A
ARG
22
n
22
ARG
22
A
ARG
23
n
23
ARG
23
A
VAL
24
n
24
VAL
24
A
ALA
25
n
25
ALA
25
A
ASP
26
n
26
ASP
26
A
GLY
27
n
27
GLY
27
A
GLU
28
n
28
GLU
28
A
ASP
29
n
29
ASP
29
A
PRO
30
n
30
PRO
30
A
LYS
31
n
31
LYS
31
A
ASP
32
n
32
ASP
32
A
VAL
33
n
33
VAL
33
A
LEU
34
n
34
LEU
34
A
ASP
35
n
35
ASP
35
A
ASP
36
n
36
ASP
36
A
LEU
37
n
37
LEU
37
A
GLY
38
n
38
GLY
38
A
LEU
39
n
39
LEU
39
A
LYS
40
n
40
LYS
40
A
ARG
41
n
41
ARG
41
A
TYR
42
n
42
TYR
42
A
CYS
43
n
43
CYS
43
A
CYS
44
n
44
CYS
44
A
ARG
45
n
45
ARG
45
A
ARG
46
n
46
ARG
46
A
MET
47
n
47
MET
47
A
LEU
48
n
48
LEU
48
A
ILE
49
n
49
ILE
49
A
SER
50
n
50
SER
50
A
HIS
51
n
51
HIS
51
A
VAL
52
n
52
VAL
52
A
GLU
53
n
53
GLU
53
A
THR
54
n
54
THR
54
A
TRP
55
n
55
TRP
55
A
author_defined_assembly
1
monomeric
A
CYS
6
A
SG
CYS
6
1_555
A
ZN
56
B
ZN
ZN
1_555
A
CYS
9
A
SG
CYS
9
1_555
111.8
A
CYS
6
A
SG
CYS
6
1_555
A
ZN
56
B
ZN
ZN
1_555
A
CYS
43
A
SG
CYS
43
1_555
113.9
A
CYS
9
A
SG
CYS
9
1_555
A
ZN
56
B
ZN
ZN
1_555
A
CYS
43
A
SG
CYS
43
1_555
104.7
A
CYS
6
A
SG
CYS
6
1_555
A
ZN
56
B
ZN
ZN
1_555
A
CYS
44
A
SG
CYS
44
1_555
111.1
A
CYS
9
A
SG
CYS
9
1_555
A
ZN
56
B
ZN
ZN
1_555
A
CYS
44
A
SG
CYS
44
1_555
112.7
A
CYS
43
A
SG
CYS
43
1_555
A
ZN
56
B
ZN
ZN
1_555
A
CYS
44
A
SG
CYS
44
1_555
102.1
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
O
H
VAL
LEU
33
37
1.54
2
A
A
O
H
VAL
LEU
33
37
1.55
3
A
A
O
H
VAL
LEU
33
37
1.56
4
A
A
O
H
VAL
LEU
33
37
1.56
5
A
A
O
H
VAL
LEU
33
37
1.54
6
A
A
O
H
VAL
LEU
33
37
1.56
7
A
A
O
H
VAL
LEU
33
37
1.54
8
A
A
O
H
VAL
LEU
33
37
1.50
9
A
A
O
H
VAL
LEU
33
37
1.54
9
A
A
O
H
SER
LYS
8
11
1.58
10
A
A
O
H
VAL
LEU
33
37
1.57
10
A
A
O
H
ARG
GLU
23
28
1.57
11
A
A
O
H
VAL
LEU
33
37
1.54
12
A
A
O
H
VAL
LEU
33
37
1.53
13
A
A
O
H
VAL
LEU
33
37
1.55
14
A
A
O
H
VAL
LEU
33
37
1.57
15
A
A
O
H
VAL
LEU
33
37
1.53
16
A
A
O
H
VAL
LEU
33
37
1.54
17
A
A
O
H
VAL
LEU
33
37
1.52
17
A
A
O
H
ASN
ARG
18
22
1.58
18
A
A
O
H
VAL
LEU
33
37
1.56
19
A
A
O
H
VAL
LEU
33
37
1.55
20
A
A
O
H
VAL
LEU
33
37
1.53
1
A
VAL
4
65.18
-76.51
1
A
ARG
5
-53.26
-178.73
1
A
SER
8
-179.40
-55.96
1
A
ASP
29
-56.72
107.62
1
A
ARG
41
63.63
132.68
1
A
HIS
51
-87.66
-73.89
1
A
VAL
52
34.93
56.19
1
A
GLU
53
-51.18
90.98
2
A
VAL
4
66.53
-67.88
2
A
ARG
5
-75.18
-168.30
2
A
CYS
6
-58.33
-157.56
2
A
LEU
7
84.74
30.94
2
A
SER
8
-174.83
-76.12
2
A
LYS
40
64.97
150.88
2
A
ARG
41
60.27
148.53
2
A
LEU
48
-70.63
-70.14
2
A
SER
50
-76.82
-78.38
2
A
VAL
52
35.57
68.05
3
A
VAL
4
60.69
159.85
3
A
ARG
5
74.13
-178.20
3
A
SER
8
177.64
-45.16
3
A
LYS
40
59.57
-80.66
3
A
ARG
46
-38.65
-39.37
3
A
VAL
52
-41.48
108.77
3
A
THR
54
53.29
80.59
4
A
VAL
4
64.45
-77.91
4
A
ARG
5
-55.86
179.27
4
A
CYS
6
-57.84
-164.38
4
A
LEU
7
93.42
28.61
4
A
SER
8
173.69
-72.92
4
A
LYS
40
-54.69
-171.82
4
A
ARG
41
84.29
-49.99
4
A
TYR
42
89.77
-23.92
4
A
ILE
49
-39.66
-32.70
4
A
HIS
51
-87.32
-77.54
4
A
VAL
52
34.26
94.43
5
A
VAL
4
64.98
-76.53
5
A
ARG
5
-55.40
-179.64
5
A
SER
8
-179.06
-60.18
5
A
SER
14
-63.20
-72.75
5
A
ASP
29
-55.67
109.83
5
A
ARG
41
-148.54
-42.09
5
A
TYR
42
89.91
-39.10
5
A
SER
50
-86.88
-76.84
5
A
VAL
52
44.99
27.70
5
A
GLU
53
47.23
75.26
6
A
VAL
4
60.93
161.66
6
A
ARG
5
79.83
-161.12
6
A
SER
8
-172.64
-61.54
6
A
LEU
39
-41.26
109.89
6
A
ARG
41
61.73
129.95
6
A
VAL
52
-40.74
108.18
7
A
VAL
4
65.56
-75.45
7
A
CYS
6
-59.68
-153.78
7
A
LEU
7
91.33
22.32
7
A
SER
8
-175.74
-70.80
7
A
ARG
41
61.44
138.07
7
A
LEU
48
-79.50
-70.25
7
A
HIS
51
-87.58
-77.36
7
A
VAL
52
35.55
97.31
7
A
THR
54
50.02
77.25
8
A
ILE
2
61.70
65.77
8
A
VAL
4
149.55
-26.55
8
A
CYS
6
-58.00
100.61
8
A
SER
8
-173.32
-75.03
8
A
ALA
15
69.27
-63.32
8
A
LYS
40
-45.69
-86.26
8
A
SER
50
-87.64
-74.04
8
A
VAL
52
45.92
76.55
8
A
GLU
53
-47.40
94.13
8
A
THR
54
-97.42
40.06
9
A
VAL
4
151.46
154.01
9
A
ARG
5
78.08
-170.29
9
A
CYS
6
-58.91
-156.65
9
A
LEU
7
83.83
34.42
9
A
SER
8
169.75
-72.58
9
A
CYS
9
47.11
27.21
9
A
LEU
39
-39.05
113.86
9
A
LYS
40
-78.16
-73.20
9
A
ARG
46
-39.51
-35.28
9
A
ILE
49
-38.26
-30.10
9
A
SER
50
-82.00
-79.05
9
A
VAL
52
42.38
29.29
9
A
GLU
53
47.75
96.89
10
A
PRO
3
-86.49
43.88
10
A
VAL
4
-170.60
-73.02
10
A
ARG
5
-57.21
175.68
10
A
SER
8
-164.75
-79.33
10
A
LYS
40
54.15
-90.06
10
A
ARG
46
-39.49
-39.32
10
A
SER
50
-87.09
-72.47
10
A
VAL
52
37.85
71.88
11
A
VAL
4
65.38
-73.43
11
A
ARG
5
-67.73
-173.36
11
A
CYS
6
-57.17
-162.12
11
A
LEU
7
92.19
32.83
11
A
SER
8
178.87
-67.93
11
A
CYS
9
48.54
25.83
11
A
LEU
39
-101.24
-160.94
11
A
LYS
40
-108.26
-88.08
11
A
LEU
48
-75.65
-70.80
11
A
ILE
49
-39.81
-31.15
11
A
SER
50
-77.76
-77.38
11
A
HIS
51
-88.02
-72.82
11
A
GLU
53
61.05
96.59
12
A
VAL
4
152.91
167.55
12
A
ARG
5
81.30
-166.62
12
A
SER
8
-170.56
-67.73
12
A
LYS
40
-67.62
-171.37
12
A
ARG
41
47.48
-174.46
12
A
TYR
42
-141.95
14.67
12
A
SER
50
-80.89
-77.84
12
A
HIS
51
-87.65
-74.70
12
A
VAL
52
44.98
28.98
12
A
GLU
53
62.56
108.80
13
A
VAL
4
64.50
-77.11
13
A
ARG
5
-52.25
-172.06
13
A
SER
8
-174.56
-55.72
13
A
ASP
29
-58.92
108.00
13
A
LYS
40
66.39
144.50
13
A
ARG
41
61.04
139.46
13
A
SER
50
-84.60
-78.60
13
A
VAL
52
46.08
29.42
13
A
GLU
53
59.20
-88.47
14
A
VAL
4
65.00
-76.86
14
A
ARG
5
-54.67
176.69
14
A
SER
8
-177.55
-69.19
14
A
LYS
40
-54.04
-172.62
14
A
ARG
41
71.65
-54.34
14
A
TYR
42
93.03
-23.42
14
A
SER
50
-84.74
-76.70
14
A
VAL
52
37.37
94.67
15
A
VAL
4
64.68
-77.13
15
A
ARG
5
-56.50
175.92
15
A
SER
8
-175.15
-62.22
15
A
ASP
29
-57.61
109.59
15
A
ARG
41
60.57
148.13
15
A
SER
50
-83.57
-77.10
15
A
HIS
51
-87.95
-77.07
15
A
VAL
52
54.36
135.61
16
A
VAL
4
64.89
-76.18
16
A
SER
8
-171.81
-72.10
16
A
ASP
29
-57.22
107.82
16
A
LYS
40
-40.33
-89.12
16
A
ARG
46
-36.78
-33.22
16
A
SER
50
-87.45
-77.89
16
A
VAL
52
43.58
95.65
17
A
VAL
4
64.81
-76.96
17
A
ARG
5
-54.74
-174.09
17
A
SER
8
-173.79
-66.71
17
A
ASP
29
-56.16
109.94
17
A
LYS
40
-56.12
-85.82
17
A
ILE
49
-38.95
-30.44
17
A
SER
50
-85.78
-77.31
17
A
GLU
53
70.63
-68.51
17
A
THR
54
52.29
96.23
18
A
VAL
4
60.75
160.93
18
A
ARG
5
80.00
-161.86
18
A
SER
8
-170.38
-64.19
18
A
ARG
41
60.94
138.09
18
A
SER
50
-82.86
-71.53
18
A
HIS
51
-87.66
-77.04
18
A
GLU
53
66.52
-160.05
19
A
VAL
4
64.84
-76.77
19
A
ARG
5
-51.95
-175.64
19
A
SER
8
-167.41
-67.56
19
A
LYS
40
58.73
155.26
19
A
ARG
41
56.95
110.29
19
A
HIS
51
-87.71
-78.09
19
A
VAL
52
32.68
100.15
19
A
THR
54
65.58
136.00
20
A
VAL
4
152.79
168.72
20
A
ARG
5
80.30
-163.24
20
A
SER
8
-173.78
-66.20
20
A
PRO
12
-38.82
134.46
20
A
ARG
23
-61.80
-72.03
20
A
LYS
40
-45.97
-78.10
20
A
SER
50
-80.26
-73.47
20
A
HIS
51
-87.20
-76.41
20
A
VAL
52
36.74
98.47
20
A
GLU
53
-47.66
101.03
SOLUTION STRUCTURE OF THE ESSENTIAL RNA POLYMERASE SUBUNIT RPB10 FROM METHANOBACTERIUM THERMOAUTOTROPHICUM
1
N
N
2
N
N
A
SER
14
A
SER
14
HELX_P
A
ASP
26
A
ASP
26
1
1
13
A
PRO
30
A
PRO
30
HELX_P
A
LEU
37
A
LEU
37
1
2
8
A
CYS
43
A
CYS
43
HELX_P
A
LEU
48
A
LEU
48
1
3
6
metalc
2.222
A
CYS
6
A
SG
CYS
6
1_555
A
ZN
56
B
ZN
ZN
1_555
metalc
2.234
A
CYS
9
A
SG
CYS
9
1_555
A
ZN
56
B
ZN
ZN
1_555
metalc
2.319
A
CYS
43
A
SG
CYS
43
1_555
A
ZN
56
B
ZN
ZN
1_555
metalc
2.300
A
CYS
44
A
SG
CYS
44
1_555
A
ZN
56
B
ZN
ZN
1_555
TRANSFERASE
THREE HELIX BUNDLE, ZINC BINDING, Structural Genomics, PSI, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, TRANSFERASE
RPON_METTH
UNP
1
O26147
1
55
1EF4
1
55
O26147
A
1
1
55
BINDING SITE FOR RESIDUE ZN A 56
A
ZN
56
Software
4
A
CYS
6
A
CYS
6
4
1_555
A
CYS
9
A
CYS
9
4
1_555
A
CYS
43
A
CYS
43
4
1_555
A
CYS
44
A
CYS
44
4
1_555
1
P 1