1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Davy, S.L.
Osborne, M.J.
Moore, G.R.
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 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 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
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
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
277
683
706
10.1006/jmbi.1998.1631
9533888
Determination of the structure of oxidised Desulfovibrio africanus ferredoxin I by 1H NMR spectroscopy and comparison of its solution structure with its crystal structure.
1998
10.2210/pdb1dax/pdb
pdb_00001dax
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
OXIDIZED
7206.928
FERREDOXIN I
1
nat
polymer
351.640
IRON/SULFUR CLUSTER
1
syn
non-polymer
no
no
ARKFYVDQDECIACESCVEIAPGAFAMDPEIEKAYVKDVEGASQEEVEEAMDTCPVQCIHWEDE
ARKFYVDQDECIACESCVEIAPGAFAMDPEIEKAYVKDVEGASQEEVEEAMDTCPVQCIHWEDE
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
Desulfovibrio
sample
873
Desulfovibrio africanus
BENGHAZI
database_2
pdbx_database_status
pdbx_nmr_exptl_sample_conditions
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Experimental preparation
Other
1
0
1999-01-13
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_exptl_sample_conditions.pressure_units
_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
1997-12-01
REL
REL
SF4
IRON/SULFUR CLUSTER
THE STRUCTURES WERE OBTAINED USING 1H-1H 2D NMR EXPERIMENTS (DQF-COSY, TOCSY, NOESY). ADDITIONALLY 1D NOE EXPERIMENTS PROVIDED INFORMATION ON THE REGIONS OF THE PROTEIN CLOSE TO THE PARAMAGNETIC 4FE-4S CLUSTER.
75
1
DQF-COSY
TOCSY
NOESY
1D NOE
7.2
1
atm
298
K
DISTANCE GEOMETRY, DG-SIMULATED ANNEALING
90%H2O/10%D2O, 99.9%D2O
GUNTERT,WUTHRICH
refinement
DIANA
2.5
structure solution
DIANA
2.5
structure solution
X-PLOR
3.843
400
JEOL
JEOL GX-400
500
Bruker
JEOL A-500
600
Varian
BRUKER AMX500 AND AMX600
600
Varian
VARIAN UNITY INOVA 600
FS4
65
2
SF4
SF4
65
A
ALA
1
n
1
ALA
1
A
ARG
2
n
2
ARG
2
A
LYS
3
n
3
LYS
3
A
PHE
4
n
4
PHE
4
A
TYR
5
n
5
TYR
5
A
VAL
6
n
6
VAL
6
A
ASP
7
n
7
ASP
7
A
GLN
8
n
8
GLN
8
A
ASP
9
n
9
ASP
9
A
GLU
10
n
10
GLU
10
A
CYS
11
n
11
CYS
11
A
ILE
12
n
12
ILE
12
A
ALA
13
n
13
ALA
13
A
CYS
14
n
14
CYS
14
A
GLU
15
n
15
GLU
15
A
SER
16
n
16
SER
16
A
CYS
17
n
17
CYS
17
A
VAL
18
n
18
VAL
18
A
GLU
19
n
19
GLU
19
A
ILE
20
n
20
ILE
20
A
ALA
21
n
21
ALA
21
A
PRO
22
n
22
PRO
22
A
GLY
23
n
23
GLY
23
A
ALA
24
n
24
ALA
24
A
PHE
25
n
25
PHE
25
A
ALA
26
n
26
ALA
26
A
MET
27
n
27
MET
27
A
ASP
28
n
28
ASP
28
A
PRO
29
n
29
PRO
29
A
GLU
30
n
30
GLU
30
A
ILE
31
n
31
ILE
31
A
GLU
32
n
32
GLU
32
A
LYS
33
n
33
LYS
33
A
ALA
34
n
34
ALA
34
A
TYR
35
n
35
TYR
35
A
VAL
36
n
36
VAL
36
A
LYS
37
n
37
LYS
37
A
ASP
38
n
38
ASP
38
A
VAL
39
n
39
VAL
39
A
GLU
40
n
40
GLU
40
A
GLY
41
n
41
GLY
41
A
ALA
42
n
42
ALA
42
A
SER
43
n
43
SER
43
A
GLN
44
n
44
GLN
44
A
GLU
45
n
45
GLU
45
A
GLU
46
n
46
GLU
46
A
VAL
47
n
47
VAL
47
A
GLU
48
n
48
GLU
48
A
GLU
49
n
49
GLU
49
A
ALA
50
n
50
ALA
50
A
MET
51
n
51
MET
51
A
ASP
52
n
52
ASP
52
A
THR
53
n
53
THR
53
A
CYS
54
n
54
CYS
54
A
PRO
55
n
55
PRO
55
A
VAL
56
n
56
VAL
56
A
GLN
57
n
57
GLN
57
A
CYS
58
n
58
CYS
58
A
ILE
59
n
59
ILE
59
A
HIS
60
n
60
HIS
60
A
TRP
61
n
61
TRP
61
A
GLU
62
n
62
GLU
62
A
ASP
63
n
63
ASP
63
A
GLU
64
n
64
GLU
64
A
author_defined_assembly
1
monomeric
A
CYS
11
A
SG
CYS
11
1_555
A
SF4
65
B
FE1
SF4
1_555
A
SF4
65
B
S2
SF4
1_555
113.8
A
CYS
11
A
SG
CYS
11
1_555
A
SF4
65
B
FE1
SF4
1_555
A
SF4
65
B
S3
SF4
1_555
116.6
A
SF4
65
B
S2
SF4
1_555
A
SF4
65
B
FE1
SF4
1_555
A
SF4
65
B
S3
SF4
1_555
108.0
A
CYS
11
A
SG
CYS
11
1_555
A
SF4
65
B
FE1
SF4
1_555
A
SF4
65
B
S4
SF4
1_555
104.6
A
SF4
65
B
S2
SF4
1_555
A
SF4
65
B
FE1
SF4
1_555
A
SF4
65
B
S4
SF4
1_555
105.0
A
SF4
65
B
S3
SF4
1_555
A
SF4
65
B
FE1
SF4
1_555
A
SF4
65
B
S4
SF4
1_555
108.0
A
CYS
14
A
SG
CYS
14
1_555
A
SF4
65
B
FE2
SF4
1_555
A
SF4
65
B
S1
SF4
1_555
100.4
A
CYS
14
A
SG
CYS
14
1_555
A
SF4
65
B
FE2
SF4
1_555
A
SF4
65
B
S3
SF4
1_555
113.9
A
SF4
65
B
S1
SF4
1_555
A
SF4
65
B
FE2
SF4
1_555
A
SF4
65
B
S3
SF4
1_555
100.3
A
CYS
14
A
SG
CYS
14
1_555
A
SF4
65
B
FE2
SF4
1_555
A
SF4
65
B
S4
SF4
1_555
136.2
A
SF4
65
B
S1
SF4
1_555
A
SF4
65
B
FE2
SF4
1_555
A
SF4
65
B
S4
SF4
1_555
98.0
A
SF4
65
B
S3
SF4
1_555
A
SF4
65
B
FE2
SF4
1_555
A
SF4
65
B
S4
SF4
1_555
101.3
A
CYS
14
A
SG
CYS
14
1_555
A
SF4
65
B
FE2
SF4
1_555
A
CYS
14
A
O
CYS
14
1_555
82.7
A
SF4
65
B
S1
SF4
1_555
A
SF4
65
B
FE2
SF4
1_555
A
CYS
14
A
O
CYS
14
1_555
118.8
A
SF4
65
B
S3
SF4
1_555
A
SF4
65
B
FE2
SF4
1_555
A
CYS
14
A
O
CYS
14
1_555
134.5
A
SF4
65
B
S4
SF4
1_555
A
SF4
65
B
FE2
SF4
1_555
A
CYS
14
A
O
CYS
14
1_555
53.6
A
CYS
17
A
SG
CYS
17
1_555
A
SF4
65
B
FE3
SF4
1_555
A
SF4
65
B
S1
SF4
1_555
102.2
A
CYS
17
A
SG
CYS
17
1_555
A
SF4
65
B
FE3
SF4
1_555
A
SF4
65
B
S2
SF4
1_555
128.3
A
SF4
65
B
S1
SF4
1_555
A
SF4
65
B
FE3
SF4
1_555
A
SF4
65
B
S2
SF4
1_555
105.3
A
CYS
17
A
SG
CYS
17
1_555
A
SF4
65
B
FE3
SF4
1_555
A
SF4
65
B
S4
SF4
1_555
113.8
A
SF4
65
B
S1
SF4
1_555
A
SF4
65
B
FE3
SF4
1_555
A
SF4
65
B
S4
SF4
1_555
107.2
A
SF4
65
B
S2
SF4
1_555
A
SF4
65
B
FE3
SF4
1_555
A
SF4
65
B
S4
SF4
1_555
98.6
A
CYS
54
A
SG
CYS
54
1_555
A
SF4
65
B
FE4
SF4
1_555
A
SF4
65
B
S1
SF4
1_555
115.1
A
CYS
54
A
SG
CYS
54
1_555
A
SF4
65
B
FE4
SF4
1_555
A
SF4
65
B
S2
SF4
1_555
119.7
A
SF4
65
B
S1
SF4
1_555
A
SF4
65
B
FE4
SF4
1_555
A
SF4
65
B
S2
SF4
1_555
104.0
A
CYS
54
A
SG
CYS
54
1_555
A
SF4
65
B
FE4
SF4
1_555
A
SF4
65
B
S3
SF4
1_555
113.2
A
SF4
65
B
S1
SF4
1_555
A
SF4
65
B
FE4
SF4
1_555
A
SF4
65
B
S3
SF4
1_555
103.1
A
SF4
65
B
S2
SF4
1_555
A
SF4
65
B
FE4
SF4
1_555
A
SF4
65
B
S3
SF4
1_555
99.4
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
ALA
26
A
O
ALA
26
A
N
TYR
35
A
N
TYR
35
1
A
A
O
H
ASP
ASP
7
9
0.23
1
A
A
OD2
HD2
ASP
PRO
28
29
1.05
1
A
A
HA
O
MET
LYS
27
33
1.07
1
A
A
HB2
HG22
ALA
VAL
42
47
1.11
1
A
A
HB
HB3
ILE
ALA
20
50
1.19
1
A
A
O
N
ASP
ASP
7
9
1.19
1
A
A
HG13
H
ILE
ALA
12
13
1.24
1
A
A
HA
HG13
TYR
VAL
5
36
1.25
1
A
A
HB3
HB3
GLU
CYS
10
58
1.28
1
A
A
HG22
CZ
VAL
PHE
6
25
1.29
1
A
A
C
H
ASP
ASP
7
9
1.32
1
A
A
HG12
HB
VAL
ILE
6
59
1.35
1
A
A
CG
HD2
ASP
PRO
28
29
1.39
1
A
A
O
HG13
TYR
ILE
5
59
1.41
1
A
A
O
HB2
GLN
GLU
44
48
1.47
1
A
A
O
HA
ASP
GLU
28
32
1.53
1
A
A
HG11
O
VAL
CYS
6
58
1.54
1
A
A
HG3
O
GLN
ALA
8
34
1.59
1
A
A
O
N
ILE
LYS
31
33
2.02
1
A
A
CA
O
MET
LYS
27
33
2.06
1
A
A
CG2
CZ
VAL
PHE
6
25
2.15
1
A
A
C
N
ASP
ASP
7
9
2.17
1
A
ARG
2
0.089
SIDE CHAIN
1
A
LYS
3
-123.94
-156.17
1
A
PHE
4
165.92
177.08
1
A
TYR
5
174.40
-160.02
1
A
GLN
8
-0.86
-0.05
1
A
ALA
13
161.87
25.77
1
A
ILE
20
-63.43
7.78
1
A
ALA
21
-178.15
66.19
1
A
PRO
22
-73.57
32.76
1
A
ALA
26
-174.62
112.47
1
A
GLU
32
14.85
43.37
1
A
CYS
58
-76.37
28.74
model building
X-PLOR
refinement
X-PLOR
phasing
X-PLOR
OXIDISED DESULFOVIBRIO AFRICANUS FERREDOXIN I, NMR, MINIMIZED AVERAGE STRUCTURE
1
Y
N
2
N
N
A
SER
16
A
SER
16
HELX_P
A
ALA
21
A
ALA
21
1
1
6
A
GLN
44
A
GLN
44
HELX_P
A
THR
53
A
THR
53
1
2
10
metalc
2.178
A
CYS
11
A
SG
CYS
11
1_555
A
SF4
65
B
FE1
SF4
1_555
metalc
2.181
A
CYS
14
A
SG
CYS
14
1_555
A
SF4
65
B
FE2
SF4
1_555
metalc
2.444
A
CYS
14
A
O
CYS
14
1_555
A
SF4
65
B
FE2
SF4
1_555
metalc
2.179
A
CYS
17
A
SG
CYS
17
1_555
A
SF4
65
B
FE3
SF4
1_555
metalc
2.179
A
CYS
54
A
SG
CYS
54
1_555
A
SF4
65
B
FE4
SF4
1_555
ELECTRON TRANSPORT
ELECTRON TRANSPORT, OXIDISED DESULFOVIBRIO AFRICANUS FERREDOXIN I, ELECTRON-TRANSFER PROTEIN, 4FE-4S CLUSTER
FER1_DESAF
UNP
1
1
P00210
ARKFYVDQDECIACESCVEIAPGAFAMDPEIEKAYVKDVEGASQEEVEEAMDTCPVQCIHWEDE
1
64
1DAX
1
64
P00210
A
1
1
64
2
anti-parallel
A
PHE
25
A
PHE
25
A
MET
27
A
MET
27
A
ALA
34
A
ALA
34
A
VAL
36
A
VAL
36
BINDING SITE FOR RESIDUE SF4 A 65
A
SF4
65
Software
7
A
CYS
11
A
CYS
11
7
1_555
A
ILE
12
A
ILE
12
7
1_555
A
CYS
14
A
CYS
14
7
1_555
A
CYS
17
A
CYS
17
7
1_555
A
ALA
34
A
ALA
34
7
1_555
A
CYS
54
A
CYS
54
7
1_555
A
CYS
58
A
CYS
58
7
1_555
1
P 1