1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Aono, S.
Bentrop, D.
Bertini, I.
Donaire, A.
Luchinat, C.
Niikura, Y.
Rosato, A.
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
Fe3 S4
295.795
FE3-S4 CLUSTER
non-polymer
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 H15 N2 O2 1
147.195
y
LYSINE
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
Fe4 S4
351.640
IRON/SULFUR CLUSTER
non-polymer
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
Biochemistry
BICHAW
0033
0006-2960
37
9812
9826
10.1021/bi972818b
9657695
Solution structure of the oxidized Fe7S8 ferredoxin from the thermophilic bacterium Bacillus schlegelii by 1H NMR spectroscopy.
1998
GW
J.Biol.Inorg.Chem.
JJBCFA
2154
0949-8257
1
523
1H NMR Studies of the Fe7S8 Ferredoxin from Bacillus Schlegelii: A Further Attempt to Understand Fe3S4 Clusters
1996
US
Biochem.Biophys.Res.Commun.
BBRCA9
0146
0006-291X
201
938
Cloning and Expression of the Gene Encoding the 7Fe Type Ferredoxin from a Thermophilic Hydrogen Oxidizing Bacterium, Bacillus Schlegelii
1994
JA
J.Biochem.(Tokyo)
JOBIAO
0418
0021-924X
112
792
Purification and Characterization of a 7Fe Ferredoxin from a Thermophilic Hydrogen-Oxidizing Bacterium, Bacillus Schlegelii
1992
10.2210/pdb1bd6/pdb
pdb_00001bd6
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
8750.828
7-FE FERREDOXIN
1
man
polymer
295.795
FE3-S4 CLUSTER
1
syn
non-polymer
351.640
IRON/SULFUR CLUSTER
1
syn
non-polymer
no
no
AYVITEPCIGTKDASCVEVCPVDCIHEGEDQYYIDPDVCIDCGACEAVCPVSAIYHEDFVPEEWKSYIQKNRDFFKK
AYVITEPCIGTKDASCVEVCPVDCIHEGEDQYYIDPDVCIDCGACEAVCPVSAIYHEDFVPEEWKSYIQKNRDFFKK
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
Bacillus
Escherichia
sample
ATCC 43741
1484
Bacillus schlegelii
562
Escherichia coli
JM 109
BACTERIUM
PKKFD54
database_2
pdbx_database_status
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
Other
1
0
1998-06-17
1
1
2008-03-24
1
2
2011-07-13
1
3
2022-02-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
_pdbx_nmr_software.name
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr2_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_atom_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
BNL
1998-05-06
REL
REL
F3S
FE3-S4 CLUSTER
SF4
IRON/SULFUR CLUSTER
300
1
NOESY
TOCSY
DQF-COSY
6.5
288
K
THE STRUCTURE CALCULATIONS WERE CARRIED OUT WITH THE PROGRAM DYANA (BY GUNTERT,MUMENTHALER,WUTHRICH). THE 20 STRUCTURES OF THE DYANA FAMILY WITH THE LOWEST TARGET FUNCTION VALUES WERE REFINED BY RESTRAINED ENERGY MINIMIZATION (REM) AND RESTRAINED MOLECULAR DYNAMICS (RMD) IN VACUO. THE STRUCTURE IN THIS ENTRY REPRESENTS THE MINIMIZED AVERAGE STRUCTURE OF THE RMD FAMILY. REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
torsion angle dynamics
PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMAN
refinement
Amber
4.1
structure solution
DYANA
500
Bruker
AMX600
600
Bruker
DRX 500
FS3
78
2
F3S
F3S
78
A
FS4
79
3
SF4
SF4
79
A
ALA
1
n
1
ALA
1
A
TYR
2
n
2
TYR
2
A
VAL
3
n
3
VAL
3
A
ILE
4
n
4
ILE
4
A
THR
5
n
5
THR
5
A
GLU
6
n
6
GLU
6
A
PRO
7
n
7
PRO
7
A
CYS
8
n
8
CYS
8
A
ILE
9
n
9
ILE
9
A
GLY
10
n
10
GLY
10
A
THR
11
n
11
THR
11
A
LYS
12
n
12
LYS
12
A
ASP
13
n
13
ASP
13
A
ALA
14
n
14
ALA
14
A
SER
15
n
15
SER
15
A
CYS
16
n
16
CYS
16
A
VAL
17
n
17
VAL
17
A
GLU
18
n
18
GLU
18
A
VAL
19
n
19
VAL
19
A
CYS
20
n
20
CYS
20
A
PRO
21
n
21
PRO
21
A
VAL
22
n
22
VAL
22
A
ASP
23
n
23
ASP
23
A
CYS
24
n
24
CYS
24
A
ILE
25
n
25
ILE
25
A
HIS
26
n
26
HIS
26
A
GLU
27
n
27
GLU
27
A
GLY
28
n
28
GLY
28
A
GLU
29
n
29
GLU
29
A
ASP
30
n
30
ASP
30
A
GLN
31
n
31
GLN
31
A
TYR
32
n
32
TYR
32
A
TYR
33
n
33
TYR
33
A
ILE
34
n
34
ILE
34
A
ASP
35
n
35
ASP
35
A
PRO
36
n
36
PRO
36
A
ASP
37
n
37
ASP
37
A
VAL
38
n
38
VAL
38
A
CYS
39
n
39
CYS
39
A
ILE
40
n
40
ILE
40
A
ASP
41
n
41
ASP
41
A
CYS
42
n
42
CYS
42
A
GLY
43
n
43
GLY
43
A
ALA
44
n
44
ALA
44
A
CYS
45
n
45
CYS
45
A
GLU
46
n
46
GLU
46
A
ALA
47
n
47
ALA
47
A
VAL
48
n
48
VAL
48
A
CYS
49
n
49
CYS
49
A
PRO
50
n
50
PRO
50
A
VAL
51
n
51
VAL
51
A
SER
52
n
52
SER
52
A
ALA
53
n
53
ALA
53
A
ILE
54
n
54
ILE
54
A
TYR
55
n
55
TYR
55
A
HIS
56
n
56
HIS
56
A
GLU
57
n
57
GLU
57
A
ASP
58
n
58
ASP
58
A
PHE
59
n
59
PHE
59
A
VAL
60
n
60
VAL
60
A
PRO
61
n
61
PRO
61
A
GLU
62
n
62
GLU
62
A
GLU
63
n
63
GLU
63
A
TRP
64
n
64
TRP
64
A
LYS
65
n
65
LYS
65
A
SER
66
n
66
SER
66
A
TYR
67
n
67
TYR
67
A
ILE
68
n
68
ILE
68
A
GLN
69
n
69
GLN
69
A
LYS
70
n
70
LYS
70
A
ASN
71
n
71
ASN
71
A
ARG
72
n
72
ARG
72
A
ASP
73
n
73
ASP
73
A
PHE
74
n
74
PHE
74
A
PHE
75
n
75
PHE
75
A
LYS
76
n
76
LYS
76
A
LYS
77
n
77
LYS
77
A
author_defined_assembly
1
monomeric
A
CYS
8
A
SG
CYS
8
1_555
A
F3S
78
B
FE1
F3S
1_555
A
F3S
78
B
S1
F3S
1_555
117.9
A
CYS
8
A
SG
CYS
8
1_555
A
F3S
78
B
FE1
F3S
1_555
A
F3S
78
B
S2
F3S
1_555
116.6
A
F3S
78
B
S1
F3S
1_555
A
F3S
78
B
FE1
F3S
1_555
A
F3S
78
B
S2
F3S
1_555
103.2
A
CYS
8
A
SG
CYS
8
1_555
A
F3S
78
B
FE1
F3S
1_555
A
F3S
78
B
S3
F3S
1_555
113.8
A
F3S
78
B
S1
F3S
1_555
A
F3S
78
B
FE1
F3S
1_555
A
F3S
78
B
S3
F3S
1_555
101.4
A
F3S
78
B
S2
F3S
1_555
A
F3S
78
B
FE1
F3S
1_555
A
F3S
78
B
S3
F3S
1_555
101.5
A
CYS
16
A
SG
CYS
16
1_555
A
F3S
78
B
FE4
F3S
1_555
A
F3S
78
B
S2
F3S
1_555
112.6
A
CYS
16
A
SG
CYS
16
1_555
A
F3S
78
B
FE4
F3S
1_555
A
F3S
78
B
S3
F3S
1_555
109.8
A
F3S
78
B
S2
F3S
1_555
A
F3S
78
B
FE4
F3S
1_555
A
F3S
78
B
S3
F3S
1_555
110.1
A
CYS
16
A
SG
CYS
16
1_555
A
F3S
78
B
FE4
F3S
1_555
A
F3S
78
B
S4
F3S
1_555
113.2
A
F3S
78
B
S2
F3S
1_555
A
F3S
78
B
FE4
F3S
1_555
A
F3S
78
B
S4
F3S
1_555
98.9
A
F3S
78
B
S3
F3S
1_555
A
F3S
78
B
FE4
F3S
1_555
A
F3S
78
B
S4
F3S
1_555
111.8
A
CYS
20
A
SG
CYS
20
1_555
A
SF4
79
C
FE1
SF4
1_555
A
SF4
79
C
S2
SF4
1_555
116.5
A
CYS
20
A
SG
CYS
20
1_555
A
SF4
79
C
FE1
SF4
1_555
A
SF4
79
C
S3
SF4
1_555
115.2
A
SF4
79
C
S2
SF4
1_555
A
SF4
79
C
FE1
SF4
1_555
A
SF4
79
C
S3
SF4
1_555
104.1
A
CYS
20
A
SG
CYS
20
1_555
A
SF4
79
C
FE1
SF4
1_555
A
SF4
79
C
S4
SF4
1_555
113.5
A
SF4
79
C
S2
SF4
1_555
A
SF4
79
C
FE1
SF4
1_555
A
SF4
79
C
S4
SF4
1_555
102.1
A
SF4
79
C
S3
SF4
1_555
A
SF4
79
C
FE1
SF4
1_555
A
SF4
79
C
S4
SF4
1_555
103.8
A
CYS
39
A
SG
CYS
39
1_555
A
SF4
79
C
FE2
SF4
1_555
A
SF4
79
C
S1
SF4
1_555
105.1
A
CYS
39
A
SG
CYS
39
1_555
A
SF4
79
C
FE2
SF4
1_555
A
SF4
79
C
S3
SF4
1_555
114.1
A
SF4
79
C
S1
SF4
1_555
A
SF4
79
C
FE2
SF4
1_555
A
SF4
79
C
S3
SF4
1_555
102.6
A
CYS
39
A
SG
CYS
39
1_555
A
SF4
79
C
FE2
SF4
1_555
A
SF4
79
C
S4
SF4
1_555
111.9
A
SF4
79
C
S1
SF4
1_555
A
SF4
79
C
FE2
SF4
1_555
A
SF4
79
C
S4
SF4
1_555
110.5
A
SF4
79
C
S3
SF4
1_555
A
SF4
79
C
FE2
SF4
1_555
A
SF4
79
C
S4
SF4
1_555
112.0
A
CYS
42
A
SG
CYS
42
1_555
A
SF4
79
C
FE3
SF4
1_555
A
SF4
79
C
S1
SF4
1_555
109.2
A
CYS
42
A
SG
CYS
42
1_555
A
SF4
79
C
FE3
SF4
1_555
A
SF4
79
C
S2
SF4
1_555
112.7
A
SF4
79
C
S1
SF4
1_555
A
SF4
79
C
FE3
SF4
1_555
A
SF4
79
C
S2
SF4
1_555
104.6
A
CYS
42
A
SG
CYS
42
1_555
A
SF4
79
C
FE3
SF4
1_555
A
SF4
79
C
S4
SF4
1_555
115.1
A
SF4
79
C
S1
SF4
1_555
A
SF4
79
C
FE3
SF4
1_555
A
SF4
79
C
S4
SF4
1_555
104.5
A
SF4
79
C
S2
SF4
1_555
A
SF4
79
C
FE3
SF4
1_555
A
SF4
79
C
S4
SF4
1_555
109.8
A
CYS
45
A
SG
CYS
45
1_555
A
SF4
79
C
FE4
SF4
1_555
A
SF4
79
C
S1
SF4
1_555
98.8
A
CYS
45
A
SG
CYS
45
1_555
A
SF4
79
C
FE4
SF4
1_555
A
SF4
79
C
S2
SF4
1_555
109.9
A
SF4
79
C
S1
SF4
1_555
A
SF4
79
C
FE4
SF4
1_555
A
SF4
79
C
S2
SF4
1_555
107.6
A
CYS
45
A
SG
CYS
45
1_555
A
SF4
79
C
FE4
SF4
1_555
A
SF4
79
C
S3
SF4
1_555
126.5
A
SF4
79
C
S1
SF4
1_555
A
SF4
79
C
FE4
SF4
1_555
A
SF4
79
C
S3
SF4
1_555
104.6
A
SF4
79
C
S2
SF4
1_555
A
SF4
79
C
FE4
SF4
1_555
A
SF4
79
C
S3
SF4
1_555
107.7
A
CYS
49
A
SG
CYS
49
1_555
A
F3S
78
B
FE3
F3S
1_555
A
F3S
78
B
S1
F3S
1_555
119.5
A
CYS
49
A
SG
CYS
49
1_555
A
F3S
78
B
FE3
F3S
1_555
A
F3S
78
B
S3
F3S
1_555
111.4
A
F3S
78
B
S1
F3S
1_555
A
F3S
78
B
FE3
F3S
1_555
A
F3S
78
B
S3
F3S
1_555
108.2
A
CYS
49
A
SG
CYS
49
1_555
A
F3S
78
B
FE3
F3S
1_555
A
F3S
78
B
S4
F3S
1_555
109.4
A
F3S
78
B
S1
F3S
1_555
A
F3S
78
B
FE3
F3S
1_555
A
F3S
78
B
S4
F3S
1_555
101.8
A
F3S
78
B
S3
F3S
1_555
A
F3S
78
B
FE3
F3S
1_555
A
F3S
78
B
S4
F3S
1_555
105.4
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
O
HIS
26
A
O
HIS
26
A
N
TYR
33
A
N
TYR
33
A
N
VAL
3
A
N
VAL
3
A
O
TYR
55
A
O
TYR
55
1
A
CA
ALA
1
WRONG HAND
1
A
TYR
32
0.085
SIDE CHAIN
1
A
TYR
33
0.090
SIDE CHAIN
1
A
PHE
74
0.089
SIDE CHAIN
1
A
PHE
75
0.076
SIDE CHAIN
1
A
GLU
6
-15.94
-66.19
1
A
LYS
12
76.07
-42.07
1
A
ALA
14
-169.58
-50.68
1
A
VAL
17
9.98
-79.04
1
A
ASP
23
40.09
22.04
1
A
ASP
30
-110.29
-72.29
1
A
ASP
41
48.15
78.83
1
A
LYS
76
-84.95
-153.71
model building
DYANA
refinement
AMBER
refinement
DYANA
7-FE FERREDOXIN FROM BACILLUS SCHLEGELII, NMR, MINIMIZED AVERAGE STRUCTURE
1
Y
N
2
N
N
3
N
N
A
GLU
6
A
GLU
6
HELX_P
A
CYS
8
A
CYS
8
5
1
3
A
VAL
17
A
VAL
17
HELX_P
A
VAL
19
A
VAL
19
5
2
3
A
ALA
44
A
ALA
44
HELX_P
A
VAL
48
A
VAL
48
1
3
5
A
PRO
50
A
PRO
50
HELX_P
A
SER
52
A
SER
52
5
4
3
A
GLU
62
A
GLU
62
HELX_P
A
PHE
75
A
PHE
75
1
5
14
metalc
2.115
A
CYS
8
A
SG
CYS
8
1_555
A
F3S
78
B
FE1
F3S
1_555
metalc
2.149
A
CYS
16
A
SG
CYS
16
1_555
A
F3S
78
B
FE4
F3S
1_555
metalc
2.052
A
CYS
20
A
SG
CYS
20
1_555
A
SF4
79
C
FE1
SF4
1_555
metalc
2.047
A
CYS
39
A
SG
CYS
39
1_555
A
SF4
79
C
FE2
SF4
1_555
metalc
2.126
A
CYS
42
A
SG
CYS
42
1_555
A
SF4
79
C
FE3
SF4
1_555
metalc
2.043
A
CYS
45
A
SG
CYS
45
1_555
A
SF4
79
C
FE4
SF4
1_555
metalc
2.189
A
CYS
49
A
SG
CYS
49
1_555
A
F3S
78
B
FE3
F3S
1_555
ELECTRON TRANSPORT
ELECTRON TRANSPORT, IRON-SULFUR
A
ALA
14
A
ALA
14
1
A
SER
15
A
SER
15
3.32
FER_BACSC
UNP
1
1
Q45560
AYVITEPCIGTKDASCVEVCPVDCIHEGEDQYYIDPDVCIDCGACEAVCPVSAIYHEDFVPEEWKSYIQKNRDFFKK
1
77
1BD6
1
77
Q45560
A
1
1
77
2
2
anti-parallel
anti-parallel
A
ILE
25
A
ILE
25
A
GLU
27
A
GLU
27
A
TYR
32
A
TYR
32
A
ILE
34
A
ILE
34
A
TYR
2
A
TYR
2
A
VAL
3
A
VAL
3
A
TYR
55
A
TYR
55
A
HIS
56
A
HIS
56
BINDING SITE FOR RESIDUE F3S A 78
A
F3S
78
Software
6
BINDING SITE FOR RESIDUE SF4 A 79
A
SF4
79
Software
7
A
ILE
4
A
ILE
4
6
1_555
A
CYS
8
A
CYS
8
6
1_555
A
SER
15
A
SER
15
6
1_555
A
CYS
16
A
CYS
16
6
1_555
A
CYS
49
A
CYS
49
6
1_555
A
ILE
54
A
ILE
54
6
1_555
A
TYR
2
A
TYR
2
7
1_555
A
CYS
20
A
CYS
20
7
1_555
A
ILE
34
A
ILE
34
7
1_555
A
CYS
39
A
CYS
39
7
1_555
A
ILE
40
A
ILE
40
7
1_555
A
CYS
42
A
CYS
42
7
1_555
A
CYS
45
A
CYS
45
7
1_555
1
P 1