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/pdb1k3h/pdb
pdb_00001k3h
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
1k3g is the Minimized family (30 conformers) of oxidized cytochrome c-553 from B. pasteurii.
1c75 is the X-ray structure of the cytochrome c-553 from B. pasteurii.
RCSB
Y
RCSB
2001-10-03
REL
REL
HEC
HEME C
1
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
97.5
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
89.9
A
HEC
93
B
NA
HEC
1_555
A
HEC
93
B
FE
HEC
1_555
A
HEC
93
B
NB
HEC
1_555
90.8
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
86.9
A
HEC
93
B
NA
HEC
1_555
A
HEC
93
B
FE
HEC
1_555
A
HEC
93
B
NC
HEC
1_555
173.9
A
HEC
93
B
NB
HEC
1_555
A
HEC
93
B
FE
HEC
1_555
A
HEC
93
B
NC
HEC
1_555
93.4
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
88.7
A
HEC
93
B
NA
HEC
1_555
A
HEC
93
B
FE
HEC
1_555
A
HEC
93
B
ND
HEC
1_555
88.1
A
HEC
93
B
NB
HEC
1_555
A
HEC
93
B
FE
HEC
1_555
A
HEC
93
B
ND
HEC
1_555
178.2
A
HEC
93
B
NC
HEC
1_555
A
HEC
93
B
FE
HEC
1_555
A
HEC
93
B
ND
HEC
1_555
87.8
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
172.3
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
81.6
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
97.7
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
93.4
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
83.6
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
LYS
31
-161.62
-43.08
1
A
SER
34
-39.76
-37.84
1
A
ALA
43
-165.12
-82.34
1
A
GLN
68
175.33
130.03
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
30
A
GLN
9
1
1
8
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
1.803
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
1.968
A
HIS
36
A
NE2
HIS
15
1_555
A
HEC
93
B
FE
HEC
1_555
metalc
2.405
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
1K3H
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
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
A
LEU
88
A
LEU
67
17
1_555