1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Banci, L.
Bertini, I.
Ciurli, S.
Dikiy, A.
Dittmer, J.
Rosato, A.
Sciara, G.
Thompsett, A.R.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C3 H7 N O2
89.093
y
ALANINE
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
C34 H34 Fe N4 O4
618.503
HEME C
non-polymer
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
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
GE
Chembiochem
1439-4227
3
299
310
10.1002/1439-7633(20020402)3:4<299::AID-CBIC299>3.0.CO;2-0
11933230
NMR solution structure, backbone mobility, and homology modeling of c-type cytochromes from gram-positive bacteria.
2002
US
Biochemistry
BICHAW
0033
0006-2960
39
13115
13126
10.1021/bi000402j
Crystal Structure of Oxidized Bacillus pasteurii cytochrome c-553 at 0.97-A Resolution
2000
GW
J.Biol.Inorg.Chem.
JJBCFA
2154
0949-8257
3
371
382
10.1007/s007750050247
Modulation of Bacillus pasteurii Cytochrome c553 Reduction Potential by Structural and Solution Parameters
1998
10.2210/pdb1k3g/pdb
pdb_00001k3g
There is a chirality error at the CA center of VAL22.
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
1
1.0
7115.937
cytochrome c-553
residues 22-92
1
man
polymer
618.503
HEME C
1
syn
non-polymer
C553
no
no
VDAEAVVQQKCISCHGGDLTGASAPAIDKAGANYSEEEILDIILNGQGGMPGGIAKGAEAEAVAAWLAEKK
VDAEAVVQQKCISCHGGDLTGASAPAIDKAGANYSEEEILDIILNGQGGMPGGIAKGAEAEAVAAWLAEKK
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
Sporosarcina
Escherichia
sample
1474
Sporosarcina pasteurii
562
Escherichia coli
DH5alpha
plasmid
pEC86
database_2
pdbx_nmr_software
pdbx_nmr_spectrometer
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
struct_conn_type
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2001-10-31
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_pdbx_nmr_spectrometer.model
_struct_conn.conn_type_id
_struct_conn.id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_label_atom_id
_struct_conn_type.id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
1c75 is the X-ray structure of the cytochrome c553 from B. pasteurii.
1k3h is the minimized average of oxidized cytochrome c-553 from B. pasteurii.
RCSB
Y
RCSB
2001-10-03
REL
REL
HEC
HEME C
target function
400
30
2D NOESY
HNHA
1D NOE
10 mM phosphate buffer
7.5
Ambient
288
K
PSEUDOCONTACT SHIFTS WERE INCLUDED AS CONSTRAINTS BY
MEANS OF MODIFIED DYANA AND SANDER MODULES
(PSEUDODYANA, PSEUDOREM) (BANCI ET AL., 1997)
torsion angle dynamics,
restrained energy minimization
1-3 mM oxidized cytochrome c-553 in 10 mM phosphate buffer
90%H2O+10%D2O;
100% D2O
Bruker
processing
XwinNMR
2.6
Xia
data analysis
XEASY
1.3.13
Guentert
structure solution
DYANA
1.5
Kollman
refinement
Amber
5.0
800
Bruker
AVANCE
700
Bruker
AVANCE
600
Bruker
AVANCE
HEC
93
2
HEC
HEC
93
A
VAL
22
n
1
VAL
22
A
ASP
23
n
2
ASP
23
A
ALA
24
n
3
ALA
24
A
GLU
25
n
4
GLU
25
A
ALA
26
n
5
ALA
26
A
VAL
27
n
6
VAL
27
A
VAL
28
n
7
VAL
28
A
GLN
29
n
8
GLN
29
A
GLN
30
n
9
GLN
30
A
LYS
31
n
10
LYS
31
A
CYS
32
n
11
CYS
32
A
ILE
33
n
12
ILE
33
A
SER
34
n
13
SER
34
A
CYS
35
n
14
CYS
35
A
HIS
36
n
15
HIS
36
A
GLY
37
n
16
GLY
37
A
GLY
38
n
17
GLY
38
A
ASP
39
n
18
ASP
39
A
LEU
40
n
19
LEU
40
A
THR
41
n
20
THR
41
A
GLY
42
n
21
GLY
42
A
ALA
43
n
22
ALA
43
A
SER
44
n
23
SER
44
A
ALA
45
n
24
ALA
45
A
PRO
46
n
25
PRO
46
A
ALA
47
n
26
ALA
47
A
ILE
48
n
27
ILE
48
A
ASP
49
n
28
ASP
49
A
LYS
50
n
29
LYS
50
A
ALA
51
n
30
ALA
51
A
GLY
52
n
31
GLY
52
A
ALA
53
n
32
ALA
53
A
ASN
54
n
33
ASN
54
A
TYR
55
n
34
TYR
55
A
SER
56
n
35
SER
56
A
GLU
57
n
36
GLU
57
A
GLU
58
n
37
GLU
58
A
GLU
59
n
38
GLU
59
A
ILE
60
n
39
ILE
60
A
LEU
61
n
40
LEU
61
A
ASP
62
n
41
ASP
62
A
ILE
63
n
42
ILE
63
A
ILE
64
n
43
ILE
64
A
LEU
65
n
44
LEU
65
A
ASN
66
n
45
ASN
66
A
GLY
67
n
46
GLY
67
A
GLN
68
n
47
GLN
68
A
GLY
69
n
48
GLY
69
A
GLY
70
n
49
GLY
70
A
MET
71
n
50
MET
71
A
PRO
72
n
51
PRO
72
A
GLY
73
n
52
GLY
73
A
GLY
74
n
53
GLY
74
A
ILE
75
n
54
ILE
75
A
ALA
76
n
55
ALA
76
A
LYS
77
n
56
LYS
77
A
GLY
78
n
57
GLY
78
A
ALA
79
n
58
ALA
79
A
GLU
80
n
59
GLU
80
A
ALA
81
n
60
ALA
81
A
GLU
82
n
61
GLU
82
A
ALA
83
n
62
ALA
83
A
VAL
84
n
63
VAL
84
A
ALA
85
n
64
ALA
85
A
ALA
86
n
65
ALA
86
A
TRP
87
n
66
TRP
87
A
LEU
88
n
67
LEU
88
A
ALA
89
n
68
ALA
89
A
GLU
90
n
69
GLU
90
A
LYS
91
n
70
LYS
91
A
LYS
92
n
71
LYS
92
A
author_defined_assembly
1
monomeric
A
HIS
36
A
NE2
HIS
15
1_555
A
HEC
93
B
FE
HEC
1_555
A
HEC
93
B
NA
HEC
1_555
98.0
A
HIS
36
A
NE2
HIS
15
1_555
A
HEC
93
B
FE
HEC
1_555
A
HEC
93
B
NB
HEC
1_555
89.5
A
HEC
93
B
NA
HEC
1_555
A
HEC
93
B
FE
HEC
1_555
A
HEC
93
B
NB
HEC
1_555
90.6
A
HIS
36
A
NE2
HIS
15
1_555
A
HEC
93
B
FE
HEC
1_555
A
HEC
93
B
NC
HEC
1_555
86.1
A
HEC
93
B
NA
HEC
1_555
A
HEC
93
B
FE
HEC
1_555
A
HEC
93
B
NC
HEC
1_555
173.8
A
HEC
93
B
NB
HEC
1_555
A
HEC
93
B
FE
HEC
1_555
A
HEC
93
B
NC
HEC
1_555
94.0
A
HIS
36
A
NE2
HIS
15
1_555
A
HEC
93
B
FE
HEC
1_555
A
HEC
93
B
ND
HEC
1_555
91.1
A
HEC
93
B
NA
HEC
1_555
A
HEC
93
B
FE
HEC
1_555
A
HEC
93
B
ND
HEC
1_555
87.5
A
HEC
93
B
NB
HEC
1_555
A
HEC
93
B
FE
HEC
1_555
A
HEC
93
B
ND
HEC
1_555
178.0
A
HEC
93
B
NC
HEC
1_555
A
HEC
93
B
FE
HEC
1_555
A
HEC
93
B
ND
HEC
1_555
87.9
A
HIS
36
A
NE2
HIS
15
1_555
A
HEC
93
B
FE
HEC
1_555
A
MET
71
A
SD
MET
50
1_555
173.2
A
HEC
93
B
NA
HEC
1_555
A
HEC
93
B
FE
HEC
1_555
A
MET
71
A
SD
MET
50
1_555
82.1
A
HEC
93
B
NB
HEC
1_555
A
HEC
93
B
FE
HEC
1_555
A
MET
71
A
SD
MET
50
1_555
97.3
A
HEC
93
B
NC
HEC
1_555
A
HEC
93
B
FE
HEC
1_555
A
MET
71
A
SD
MET
50
1_555
93.2
A
HEC
93
B
ND
HEC
1_555
A
HEC
93
B
FE
HEC
1_555
A
MET
71
A
SD
MET
50
1_555
82.2
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
CA
VAL
22
WRONG HAND
11
A
CA
VAL
22
WRONG HAND
26
A
CA
VAL
22
WRONG HAND
11
A
A
VAL
ASP
22
23
133.18
5
A
TYR
55
0.084
SIDE CHAIN
9
A
TYR
55
0.070
SIDE CHAIN
23
A
TYR
55
0.087
SIDE CHAIN
1
11.61
1.90
111.40
123.01
A
A
A
CB
CA
C
VAL
VAL
VAL
22
22
22
N
1
9.09
1.50
110.90
119.99
A
A
A
CA
CB
CG2
VAL
VAL
VAL
22
22
22
N
26
12.14
1.90
111.40
123.54
A
A
A
CB
CA
C
VAL
VAL
VAL
22
22
22
N
26
10.91
1.50
110.90
121.81
A
A
A
CA
CB
CG2
VAL
VAL
VAL
22
22
22
N
1
A
GLN
29
-57.34
-8.03
1
A
LYS
31
-138.97
-59.44
1
A
ALA
43
-131.27
-77.93
1
A
GLN
68
177.37
135.64
2
A
GLN
30
-142.60
59.23
2
A
LYS
31
-173.08
-36.39
2
A
ALA
43
-143.79
-71.56
2
A
GLN
68
173.83
133.56
3
A
GLN
29
-58.12
-7.20
3
A
GLN
30
-142.82
33.10
3
A
LYS
31
-153.92
-55.66
3
A
ALA
43
-137.45
-75.83
3
A
GLN
68
176.87
140.58
4
A
LYS
31
-172.04
-38.58
4
A
SER
34
-38.92
-36.75
4
A
ALA
43
-143.52
-76.90
4
A
LYS
50
-109.31
40.87
4
A
GLN
68
176.31
131.38
4
A
GLU
90
-84.70
35.65
5
A
GLN
30
-146.43
48.60
5
A
LYS
31
-162.46
-39.70
5
A
SER
34
-37.38
-39.19
5
A
ALA
43
-143.60
-79.77
5
A
GLN
68
173.98
130.18
6
A
GLN
30
-142.56
44.57
6
A
LYS
31
-157.36
-39.98
6
A
ALA
43
-151.79
-73.10
6
A
GLN
68
176.51
136.28
7
A
LYS
31
-161.28
-58.61
7
A
ALA
43
-152.52
-80.34
7
A
GLN
68
170.46
139.13
8
A
LYS
31
-167.96
-38.97
8
A
SER
34
-37.92
-38.55
8
A
ALA
43
-135.39
-78.10
8
A
GLN
68
174.30
132.87
9
A
GLN
30
-141.71
43.67
9
A
LYS
31
-153.18
-39.73
9
A
SER
34
-37.75
-37.01
9
A
ALA
43
-155.08
-72.98
9
A
GLN
68
167.08
139.63
10
A
LYS
31
-166.43
-38.90
10
A
SER
34
-36.92
-39.31
10
A
ALA
43
-156.24
-76.77
10
A
GLN
68
167.03
140.72
11
A
GLN
30
-144.67
55.10
11
A
LYS
31
-167.25
-38.29
11
A
ALA
43
-135.95
-79.55
11
A
GLN
68
166.73
138.38
12
A
ALA
24
-105.18
-64.12
12
A
LYS
31
-152.37
-56.67
12
A
ALA
43
-152.92
-81.92
12
A
GLN
68
173.27
133.41
13
A
LYS
31
-157.08
-47.31
13
A
ALA
43
-128.50
-78.74
13
A
GLN
68
169.25
138.62
14
A
LYS
31
-135.86
-62.79
14
A
ALA
43
-134.50
-79.44
14
A
GLN
68
170.12
138.18
15
A
GLN
30
-144.98
48.21
15
A
LYS
31
-162.69
-49.28
15
A
ALA
43
-145.35
-78.34
15
A
GLN
68
165.70
129.74
15
A
GLU
90
-90.28
36.78
16
A
GLN
30
-141.01
56.73
16
A
LYS
31
-170.47
-38.12
16
A
SER
34
-38.64
-35.76
16
A
ALA
43
-136.42
-75.82
16
A
GLN
68
168.52
130.94
17
A
GLN
30
-150.36
50.65
17
A
LYS
31
-167.24
-37.34
17
A
ALA
43
-138.39
-79.97
17
A
GLN
68
178.29
135.65
18
A
GLN
30
-141.77
47.76
18
A
LYS
31
-166.71
-42.70
18
A
SER
34
-38.47
-37.31
18
A
ALA
43
-156.33
-78.03
18
A
GLN
68
172.46
136.45
19
A
GLN
30
-141.26
51.56
19
A
LYS
31
-162.68
-36.63
19
A
ALA
43
-156.80
-76.89
19
A
GLN
68
174.63
141.72
20
A
LYS
31
-172.20
-36.46
20
A
ALA
43
-150.15
-80.38
20
A
GLN
68
170.45
135.49
21
A
LYS
31
-148.96
-66.85
21
A
ALA
43
-145.40
-73.87
21
A
ASN
54
-103.83
-61.78
21
A
GLN
68
165.62
136.04
22
A
GLN
29
-49.78
-19.39
22
A
LYS
31
-145.96
-56.92
22
A
ALA
43
-154.23
-81.36
23
A
LYS
31
-168.50
-59.18
23
A
LEU
40
80.16
15.29
23
A
ALA
43
-164.80
-72.94
23
A
GLN
68
170.72
137.45
24
A
LYS
31
-178.22
-36.11
24
A
ALA
43
-160.67
-79.82
24
A
GLN
68
168.48
127.10
25
A
GLN
30
-141.48
34.06
25
A
LYS
31
-152.00
-62.62
25
A
ALA
43
-150.88
-73.00
25
A
GLN
68
167.41
133.36
26
A
LYS
31
-163.50
-34.19
26
A
ALA
43
-163.21
-79.16
26
A
GLN
68
175.34
131.10
27
A
ALA
24
-97.73
-61.94
27
A
GLN
30
-142.62
59.04
27
A
LYS
31
-179.81
-36.28
27
A
SER
34
-38.17
-35.53
27
A
ALA
43
-134.31
-80.13
27
A
ASP
49
-38.99
-38.29
27
A
GLN
68
171.66
133.01
28
A
LYS
31
-173.82
-36.74
28
A
SER
34
-37.82
-38.45
28
A
ALA
43
-134.86
-78.42
28
A
GLN
68
164.68
141.22
29
A
GLN
30
-149.15
58.14
29
A
LYS
31
178.34
-35.34
29
A
SER
34
-38.23
-37.15
29
A
ALA
43
-136.73
-75.47
29
A
GLN
68
173.22
131.85
30
A
ALA
24
-105.78
-62.39
30
A
LYS
31
-146.59
-48.43
30
A
ALA
43
-156.77
-79.94
30
A
GLN
68
174.58
133.95
NMR Solution Structure of Oxidized Cytochrome c-553 from Bacillus pasteurii
1
N
N
2
N
N
A
ASP
23
A
ASP
2
HELX_P
A
GLN
29
A
GLN
8
1
1
7
A
CYS
32
A
CYS
11
HELX_P
A
GLY
37
A
GLY
16
1
2
6
A
LYS
50
A
LYS
29
HELX_P
A
TYR
55
A
TYR
34
1
3
6
A
SER
56
A
SER
35
HELX_P
A
GLY
67
A
GLY
46
1
4
12
A
GLY
78
A
GLY
57
HELX_P
A
LYS
91
A
LYS
70
1
5
14
covale
1.806
none
A
CYS
32
A
SG
CYS
11
1_555
A
HEC
93
B
CAB
HEC
1_555
covale
1.813
none
A
CYS
35
A
SG
CYS
14
1_555
A
HEC
93
B
CAC
HEC
1_555
metalc
1.982
A
HIS
36
A
NE2
HIS
15
1_555
A
HEC
93
B
FE
HEC
1_555
metalc
2.407
A
MET
71
A
SD
MET
50
1_555
A
HEC
93
B
FE
HEC
1_555
ELECTRON TRANSPORT
C-553, HEME, CYTOCHROME, BACILLUS PASTEURII, ELECTRON TRANSFER, ELECTRON TRANSPORT
CY553_BACPA
UNP
1
22
P82599
VDAEAVVQQKCISCHGGDLTGASAPAIDKAGANYSEEEILDIILNGQGGMPGGIAKGAEAEAVAAWLAEKK
22
92
1K3G
22
92
P82599
A
1
1
71
BINDING SITE FOR RESIDUE HEC A 93
A
HEC
93
Software
17
A
LYS
31
A
LYS
10
17
1_555
A
CYS
32
A
CYS
11
17
1_555
A
CYS
35
A
CYS
14
17
1_555
A
HIS
36
A
HIS
15
17
1_555
A
ALA
45
A
ALA
24
17
1_555
A
PRO
46
A
PRO
25
17
1_555
A
ILE
48
A
ILE
27
17
1_555
A
TYR
55
A
TYR
34
17
1_555
A
ILE
60
A
ILE
39
17
1_555
A
ILE
63
A
ILE
42
17
1_555
A
ILE
64
A
ILE
43
17
1_555
A
GLN
68
A
GLN
47
17
1_555
A
GLY
69
A
GLY
48
17
1_555
A
GLY
70
A
GLY
49
17
1_555
A
MET
71
A
MET
50
17
1_555
A
ILE
75
A
ILE
54
17
1_555
A
VAL
84
A
VAL
63
17
1_555