1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Maciejewski, M.W.
Prasad, R.
Liu, D.-J.
Wilson, S.H.
Mullen, G.P.
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
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
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
296
229
253
10.1006/jmbi.1999.3455
10656829
Backbone dynamics and refined solution structure of the N-terminal domain of DNA polymerase beta. Correlation with DNA binding and dRP lyase activity.
2000
US
Biochemistry
BICHAW
0033
0006-2960
35
6188
6200
10.1021/bi952656o
Three-Dimensional Solution Structure of the N-terminal Domain of DNA Polymerase beta and Mapping of the ssDNA Interaction Interface
1996
US
Biochemistry
BICHAW
0033
0006-2960
33
9537
9545
Assignments of 1H, 15N, and 13C Resonances for the Backbone and Side Chains of the N-terminal domain of DNA Polymerase beta. Determination of the Secondary Structure and Tertiary Contacts.
1994
10.2210/pdb1dk3/pdb
pdb_00001dk3
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
9632.298
DNA POLYMERASE BETA
2.7.7.7
N-TERMINAL DOMAIN, RESIDUES 1-87
1
man
polymer
E.C.2.7.7.7
no
no
MSKRKAPQETLNGGITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATG
KLRKLEK
MSKRKAPQETLNGGITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATG
KLRKLEK
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
Norway rat
Rattus
Escherichia
sample
10116
Rattus norvegicus
562
Escherichia coli
PLASMID
PRSET-8K
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
2000-02-14
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
THIS IS THE PREVIOUS MINIMIZED AVERAGE STRUCTURE.
THIS IS A PREVIOUS GROUP OF 55 STRUCTURAL CONFORMERS.
RCSB
Y
RCSB
1999-12-06
REL
PROTEOLYTIC PROCESSING REMOVES THE N-TERMINAL MET IN A BACTERIAL EXPRESSION
SYSTEM (SEE KUMAR ET AL., (1990) J. BIOL. CHEM. 265, 2124-2131).
1
2D NOESY
3D_15N-SEPARATED_NOESY
3D_13C-SEPARATED_NOESY
HMQC-J
400
6.7
AMBIENT
300
K
100
6.8
AMBIENT
298
K
THE NMR RESTRAINTS INCLUDED 921 USEFUL NOE DETERMINED UPPER DISTANCE
RESTRAINTS, 41 HYDROGEN BONDS, AND 135 PHI AND CHI TORSION ANGLE RESTRAINTS.
STRUCTURES WERE CALCULATED IN THE PROGRAM DYANA USING TORSION ANGLE DYNAMICS.
THE CALCULATION STARTED WITH 100 RANDOMIZED STRUCTURES. THE 50 STRUCTURES WITH
THE LOWEST TARGET FUNCTION WERE THEN REFINED WITHIN XPLOR USING SIMULATED
ANNEALING. THE 25 LOWEST ENERGY STRUCTURAL CONFORMERS WERE SELECTED TO
REPRESENT THE ENSEMBLE.THE 25 REFINED STRUCTURAL CONFORMERS DISPLAYED NO NOE
VIOLATIONS >0.3 ANGSTROMS AND NO DIHEDRAL ANGLE VIOLATIONS >3 DEGREES. THE
MINIMIZED AVERAGE STRUCTURE WAS CALCULATED FROM THE MEAN POSITION OF THE
COORDINATES FOR THE 25 STRUCTURAL CONFORMERS AND WAS REFINED BY POWELL ENERGY
MINIMIZATION IN XPLOR USING FULL NMR RESTRAINTS.
TORSION ANGLE DYNAMICS AND SIMULATED ANNEALING
1
minimized average structure
2.8 MM RAT DNA POLYMERASE BETA N-TERMINAL DOMAIN (2-87) U-15N,13C; 5MM TRIS-
D11; 400MM NACL
2 MM RAT DNA POLYMERASE BETA N-TERMINAL DOMAIN (2-87) U-15N; 5MM TRIS-D11;
100MM NACL
4 MM RAT DNA POLYMERASE BETA N-TERMINAL DOMAIN (2-87) U-15N; 5MM TRIS-D11;
400MM NACL
2.8 MM RAT DNA POLYMERASE BETA N-TERMINAL DOMAIN (2-87) U-15N,13C; 5MM TRIS-
D11; 400MM NACL
1.4 MM RAT DNA POLYMERASE BETA N-TERMINAL DOMAIN (2-87); 5MM TRIS-D11; 400MM
NACL
VARIAN
collection
VNMR
4.3
HARE, BIOSYM
processing
Felix
95
BARTLES
data analysis
XEASY
1.3.13
GUENTERT
structure solution
DYANA
1.5
BRUNGER
refinement
X-PLOR
4.0
500
GE
GN500
600
Varian
UNITYPLUS
MET
1
n
1
MET
1
A
SER
2
n
2
SER
2
A
LYS
3
n
3
LYS
3
A
ARG
4
n
4
ARG
4
A
LYS
5
n
5
LYS
5
A
ALA
6
n
6
ALA
6
A
PRO
7
n
7
PRO
7
A
GLN
8
n
8
GLN
8
A
GLU
9
n
9
GLU
9
A
THR
10
n
10
THR
10
A
LEU
11
n
11
LEU
11
A
ASN
12
n
12
ASN
12
A
GLY
13
n
13
GLY
13
A
GLY
14
n
14
GLY
14
A
ILE
15
n
15
ILE
15
A
THR
16
n
16
THR
16
A
ASP
17
n
17
ASP
17
A
MET
18
n
18
MET
18
A
LEU
19
n
19
LEU
19
A
VAL
20
n
20
VAL
20
A
GLU
21
n
21
GLU
21
A
LEU
22
n
22
LEU
22
A
ALA
23
n
23
ALA
23
A
ASN
24
n
24
ASN
24
A
PHE
25
n
25
PHE
25
A
GLU
26
n
26
GLU
26
A
LYS
27
n
27
LYS
27
A
ASN
28
n
28
ASN
28
A
VAL
29
n
29
VAL
29
A
SER
30
n
30
SER
30
A
GLN
31
n
31
GLN
31
A
ALA
32
n
32
ALA
32
A
ILE
33
n
33
ILE
33
A
HIS
34
n
34
HIS
34
A
LYS
35
n
35
LYS
35
A
TYR
36
n
36
TYR
36
A
ASN
37
n
37
ASN
37
A
ALA
38
n
38
ALA
38
A
TYR
39
n
39
TYR
39
A
ARG
40
n
40
ARG
40
A
LYS
41
n
41
LYS
41
A
ALA
42
n
42
ALA
42
A
ALA
43
n
43
ALA
43
A
SER
44
n
44
SER
44
A
VAL
45
n
45
VAL
45
A
ILE
46
n
46
ILE
46
A
ALA
47
n
47
ALA
47
A
LYS
48
n
48
LYS
48
A
TYR
49
n
49
TYR
49
A
PRO
50
n
50
PRO
50
A
HIS
51
n
51
HIS
51
A
LYS
52
n
52
LYS
52
A
ILE
53
n
53
ILE
53
A
LYS
54
n
54
LYS
54
A
SER
55
n
55
SER
55
A
GLY
56
n
56
GLY
56
A
ALA
57
n
57
ALA
57
A
GLU
58
n
58
GLU
58
A
ALA
59
n
59
ALA
59
A
LYS
60
n
60
LYS
60
A
LYS
61
n
61
LYS
61
A
LEU
62
n
62
LEU
62
A
PRO
63
n
63
PRO
63
A
GLY
64
n
64
GLY
64
A
VAL
65
n
65
VAL
65
A
GLY
66
n
66
GLY
66
A
THR
67
n
67
THR
67
A
LYS
68
n
68
LYS
68
A
ILE
69
n
69
ILE
69
A
ALA
70
n
70
ALA
70
A
GLU
71
n
71
GLU
71
A
LYS
72
n
72
LYS
72
A
ILE
73
n
73
ILE
73
A
ASP
74
n
74
ASP
74
A
GLU
75
n
75
GLU
75
A
PHE
76
n
76
PHE
76
A
LEU
77
n
77
LEU
77
A
ALA
78
n
78
ALA
78
A
THR
79
n
79
THR
79
A
GLY
80
n
80
GLY
80
A
LYS
81
n
81
LYS
81
A
LEU
82
n
82
LEU
82
A
ARG
83
n
83
ARG
83
A
LYS
84
n
84
LYS
84
A
LEU
85
n
85
LEU
85
A
GLU
86
n
86
GLU
86
A
LYS
87
n
87
LYS
87
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
SER
2
60.10
99.50
1
A
LYS
3
84.83
-40.85
1
A
LEU
11
-89.60
-72.79
1
A
ASN
12
-104.73
44.28
1
A
SER
30
-77.27
-70.48
1
A
ALA
32
-150.81
57.26
1
A
ALA
78
-61.80
-79.46
1
A
ARG
83
-63.43
-179.31
1
A
LYS
84
-98.54
34.78
1
A
GLU
86
-98.65
34.51
minimized average
REFINED SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF DNA POLYMERASE BETA
1
N
N
A
GLY
14
A
GLY
14
HELX_P
A
VAL
29
A
VAL
29
1
1
16
A
ILE
33
A
ILE
33
HELX_P
A
LYS
48
A
LYS
48
1
2
16
A
SER
55
A
SER
55
HELX_P
A
LYS
61
A
LYS
61
1
3
7
A
THR
67
A
THR
67
HELX_P
A
THR
79
A
THR
79
1
4
13
TRANSFERASE
DNA-BINDING, DEOXYRIBOSE 5'-PHOSPHATE LYASE, NUCLEOTIDYLTRANSFERASE, TRANSFERASE
DPOB_RAT
UNP
1
P06766
1
87
1DK3
1
87
P06766
A
1
1
87
1
P 1