0.028596
0.000000
0.000000
0.000000
0.016358
0.000000
0.000000
0.000000
0.014206
0.00000
0.00000
0.00000
Zhang, X.C.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
34.970
61.134
70.391
C2 H4 O2
60.052
ACETIC ACID
non-polymer
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
Cd 2
112.411
CADMIUM ION
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
H2 O
18.015
WATER
non-polymer
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
US
Biochem.Biophys.Res.Commun.
BBRCA9
0146
1090-2104
450
929
935
10.1016/j.bbrc.2014.06.053
24952155
Atomic resolution structure of the E. coli YajR transporter YAM domain.
2014
10.2210/pdb4q2l/pdb
pdb_00004q2l
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
CCD
2012-10-23
ADSC QUANTUM 270
SAGITALLY FOCUSED Si(111)
SINGLE WAVELENGTH
M
x-ray
1
0.9500
1.0
BL-17A
Photon Factory
0.9500
SYNCHROTRON
PHOTON FACTORY BEAMLINE BL-17A
7858.906
Major facilitator superfamily MFS_1
YAM domain, UNP residues 388-454
1
man
polymer
60.052
ACETIC ACID
2
syn
non-polymer
112.411
CADMIUM ION
2
syn
non-polymer
18.015
water
89
nat
water
Predicted transporter, YajR MFS transporter
no
no
GSHMKEPPYVSSLRIEIPADIAANEALKVRLLETEGVKEVLIAEEEHSAYVKIDSKVTNRFEVEQAIRQA
GSHMKEPPYVSSLRIEIPADIAANEALKVRLLETEGVKEVLIAEEEHSAYVKIDSKVTNRFEVEQAIRQA
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
B / BL21-DE3
sample
B21_00379, E. coli, ECBD_3234, ECD_00375, yajR
469008
Escherichia coli
562
Escherichia coli
BL21
pET-28a
1
2.39
48.61
VAPOR DIFFUSION, HANGING DROP
7.5
0.1M HEPES (pH 7.5), 50mM CdSO4, 1.0M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 289K
289
citation
database_2
pdbx_struct_conn_angle
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Database references
Derived calculations
1
0
2014-07-09
1
1
2022-08-24
_citation.journal_volume
_citation.page_first
_citation.page_last
_citation.title
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_alt_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_alt_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_ptnr1_label_alt_id
_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_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Similar protein folding.
RCSB
Y
PDBJ
2014-04-09
REL
REL
ACY
ACETIC ACID
CD
CADMIUM ION
HOH
water
ACY
3004
2
ACY
ACY
101
A
ACY
3005
2
ACY
ACY
102
A
CD
2001
3
CD
CD
103
A
CD
2002
3
CD
CD
104
A
HOH
1001
4
HOH
HOH
1001
A
HOH
1002
4
HOH
HOH
1002
A
HOH
1003
4
HOH
HOH
1003
A
HOH
1004
4
HOH
HOH
1004
A
HOH
1005
4
HOH
HOH
1005
A
HOH
1006
4
HOH
HOH
1006
A
HOH
1007
4
HOH
HOH
1007
A
HOH
1008
4
HOH
HOH
1008
A
HOH
1009
4
HOH
HOH
1009
A
HOH
1010
4
HOH
HOH
1010
A
HOH
1011
4
HOH
HOH
1011
A
HOH
1012
4
HOH
HOH
1012
A
HOH
1013
4
HOH
HOH
1013
A
HOH
1014
4
HOH
HOH
1014
A
HOH
1015
4
HOH
HOH
1015
A
HOH
1016
4
HOH
HOH
1016
A
HOH
1017
4
HOH
HOH
1017
A
HOH
1018
4
HOH
HOH
1018
A
HOH
1019
4
HOH
HOH
1019
A
HOH
1020
4
HOH
HOH
1020
A
HOH
1021
4
HOH
HOH
1021
A
HOH
1022
4
HOH
HOH
1022
A
HOH
1023
4
HOH
HOH
1023
A
HOH
1024
4
HOH
HOH
1024
A
HOH
1025
4
HOH
HOH
1025
A
HOH
1026
4
HOH
HOH
1026
A
HOH
1027
4
HOH
HOH
1027
A
HOH
1028
4
HOH
HOH
1028
A
HOH
1029
4
HOH
HOH
1029
A
HOH
1030
4
HOH
HOH
1030
A
HOH
1031
4
HOH
HOH
1031
A
HOH
1032
4
HOH
HOH
1032
A
HOH
1033
4
HOH
HOH
1033
A
HOH
1034
4
HOH
HOH
1034
A
HOH
1035
4
HOH
HOH
1035
A
HOH
1036
4
HOH
HOH
1036
A
HOH
1037
4
HOH
HOH
1037
A
HOH
1038
4
HOH
HOH
1038
A
HOH
1039
4
HOH
HOH
1039
A
HOH
1040
4
HOH
HOH
1040
A
HOH
1041
4
HOH
HOH
1041
A
HOH
1042
4
HOH
HOH
1042
A
HOH
1043
4
HOH
HOH
1043
A
HOH
1044
4
HOH
HOH
1044
A
HOH
1045
4
HOH
HOH
1045
A
HOH
1046
4
HOH
HOH
1046
A
HOH
1047
4
HOH
HOH
1047
A
HOH
1048
4
HOH
HOH
1048
A
HOH
1049
4
HOH
HOH
1049
A
HOH
1050
4
HOH
HOH
1050
A
HOH
1051
4
HOH
HOH
1051
A
HOH
1052
4
HOH
HOH
1052
A
HOH
1053
4
HOH
HOH
1053
A
HOH
1054
4
HOH
HOH
1054
A
HOH
1055
4
HOH
HOH
1055
A
HOH
1056
4
HOH
HOH
1056
A
HOH
1057
4
HOH
HOH
1057
A
HOH
1058
4
HOH
HOH
1058
A
HOH
1059
4
HOH
HOH
1059
A
HOH
1060
4
HOH
HOH
1060
A
HOH
1061
4
HOH
HOH
1061
A
HOH
1062
4
HOH
HOH
1062
A
HOH
1063
4
HOH
HOH
1063
A
HOH
1064
4
HOH
HOH
1064
A
HOH
1065
4
HOH
HOH
1065
A
HOH
1066
4
HOH
HOH
1066
A
HOH
1067
4
HOH
HOH
1067
A
HOH
1068
4
HOH
HOH
1068
A
HOH
1069
4
HOH
HOH
1069
A
HOH
1070
4
HOH
HOH
1070
A
HOH
1071
4
HOH
HOH
1071
A
HOH
1072
4
HOH
HOH
1072
A
HOH
1073
4
HOH
HOH
1073
A
HOH
1074
4
HOH
HOH
1074
A
HOH
1075
4
HOH
HOH
1075
A
HOH
1076
4
HOH
HOH
1076
A
HOH
1077
4
HOH
HOH
1077
A
HOH
1078
4
HOH
HOH
1078
A
HOH
1079
4
HOH
HOH
1079
A
HOH
1080
4
HOH
HOH
1080
A
HOH
1081
4
HOH
HOH
1081
A
HOH
1082
4
HOH
HOH
1082
A
HOH
1083
4
HOH
HOH
1083
A
HOH
1084
4
HOH
HOH
1084
A
HOH
1085
4
HOH
HOH
1085
A
HOH
1086
4
HOH
HOH
1086
A
HOH
1087
4
HOH
HOH
1087
A
HOH
1088
4
HOH
HOH
1088
A
HOH
1089
4
HOH
HOH
1089
A
n
1
-2
A
n
2
-1
A
n
3
0
A
n
4
1
A
n
5
2
A
n
6
3
A
PRO
4
n
7
PRO
4
A
PRO
5
n
8
PRO
5
A
TYR
6
n
9
TYR
6
A
VAL
7
n
10
VAL
7
A
SER
8
n
11
SER
8
A
SER
9
n
12
SER
9
A
LEU
10
n
13
LEU
10
A
ARG
11
n
14
ARG
11
A
ILE
12
n
15
ILE
12
A
GLU
13
n
16
GLU
13
A
ILE
14
n
17
ILE
14
A
PRO
15
n
18
PRO
15
A
ALA
16
n
19
ALA
16
A
ASP
17
n
20
ASP
17
A
ILE
18
n
21
ILE
18
A
ALA
19
n
22
ALA
19
A
ALA
20
n
23
ALA
20
A
ASN
21
n
24
ASN
21
A
GLU
22
n
25
GLU
22
A
ALA
23
n
26
ALA
23
A
LEU
24
n
27
LEU
24
A
LYS
25
n
28
LYS
25
A
VAL
26
n
29
VAL
26
A
ARG
27
n
30
ARG
27
A
LEU
28
n
31
LEU
28
A
LEU
29
n
32
LEU
29
A
GLU
30
n
33
GLU
30
A
THR
31
n
34
THR
31
A
GLU
32
n
35
GLU
32
A
GLY
33
n
36
GLY
33
A
VAL
34
n
37
VAL
34
A
LYS
35
n
38
LYS
35
A
GLU
36
n
39
GLU
36
A
VAL
37
n
40
VAL
37
A
LEU
38
n
41
LEU
38
A
ILE
39
n
42
ILE
39
A
ALA
40
n
43
ALA
40
A
GLU
41
n
44
GLU
41
A
GLU
42
n
45
GLU
42
A
GLU
43
n
46
GLU
43
A
HIS
44
n
47
HIS
44
A
SER
45
n
48
SER
45
A
ALA
46
n
49
ALA
46
A
TYR
47
n
50
TYR
47
A
VAL
48
n
51
VAL
48
A
LYS
49
n
52
LYS
49
A
ILE
50
n
53
ILE
50
A
ASP
51
n
54
ASP
51
A
SER
52
n
55
SER
52
A
LYS
53
n
56
LYS
53
A
VAL
54
n
57
VAL
54
A
THR
55
n
58
THR
55
A
ASN
56
n
59
ASN
56
A
ARG
57
n
60
ARG
57
A
PHE
58
n
61
PHE
58
A
GLU
59
n
62
GLU
59
A
VAL
60
n
63
VAL
60
A
GLU
61
n
64
GLU
61
A
GLN
62
n
65
GLN
62
A
ALA
63
n
66
ALA
63
A
ILE
64
n
67
ILE
64
A
ARG
65
n
68
ARG
65
A
GLN
66
n
69
GLN
66
A
ALA
67
n
70
ALA
67
A
author_and_software_defined_assembly
PISA
2
dimeric
1210
-29
7810
A
GLU
13
A
A
OE2
GLU
16
1_555
A
CD
104
E
CD
CD
1_555
A
GLU
43
A
O
GLU
46
1_555
89.2
A
GLU
13
A
A
OE2
GLU
16
1_555
A
CD
104
E
CD
CD
1_555
A
HOH
1035
F
O
HOH
1_555
86.1
A
GLU
43
A
O
GLU
46
1_555
A
CD
104
E
CD
CD
1_555
A
HOH
1035
F
O
HOH
1_555
89.3
A
GLU
13
A
A
OE2
GLU
16
1_555
A
CD
104
E
CD
CD
1_555
A
HOH
1088
F
O
HOH
1_555
80.3
A
GLU
43
A
O
GLU
46
1_555
A
CD
104
E
CD
CD
1_555
A
HOH
1088
F
O
HOH
1_555
165.7
A
HOH
1035
F
O
HOH
1_555
A
CD
104
E
CD
CD
1_555
A
HOH
1088
F
O
HOH
1_555
99.6
A
HIS
44
A
ND1
HIS
47
1_555
A
CD
103
D
CD
CD
1_555
A
ACY
101
B
O
ACY
1_555
141.5
A
HIS
44
A
ND1
HIS
47
1_555
A
CD
103
D
CD
CD
1_555
A
HOH
1039
F
O
HOH
1_555
95.7
A
ACY
101
B
O
ACY
1_555
A
CD
103
D
CD
CD
1_555
A
HOH
1039
F
O
HOH
1_555
83.8
A
HIS
44
A
ND1
HIS
47
1_555
A
CD
103
D
CD
CD
1_555
A
HOH
1040
F
O
HOH
1_555
89.2
A
ACY
101
B
O
ACY
1_555
A
CD
103
D
CD
CD
1_555
A
HOH
1040
F
O
HOH
1_555
88.4
A
HOH
1039
F
O
HOH
1_555
A
CD
103
D
CD
CD
1_555
A
HOH
1040
F
O
HOH
1_555
172.0
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
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
4_575
x,-y+2,-z
crystal symmetry operation
0.0000000000
122.2680000000
0.0000000000
A
N
ILE
12
A
N
ILE
15
A
O
ALA
46
A
O
ALA
49
A
O
LYS
49
A
O
LYS
52
A
N
LYS
35
A
N
LYS
38
1
A
HOH
1037
F
HOH
1
A
HOH
1045
F
HOH
1
A
HOH
1078
F
HOH
1
A
GLY
-2
A
GLY
1
1
Y
1
A
SER
-1
A
SER
2
1
Y
1
A
HIS
0
A
HIS
3
1
Y
1
A
MET
1
A
MET
4
1
Y
1
A
LYS
2
A
LYS
5
1
Y
1
A
GLU
3
A
GLU
6
1
Y
1
A
A
O
O
HOH
HOH
1058
1083
2.08
1
A
A
OE1
O
GLU
HOH
61
1081
2.08
A
1
A
A
O
OG
TYR
SER
6
52
2.10
1
A
A
NZ
O
LYS
HOH
35
1084
2.12
1
A
A
NZ
O
LYS
HOH
25
1042
2.19
B
1
12.86
2.10
128.40
141.26
A
A
A
C
N
CD
PRO
PRO
PRO
4
5
5
Y
1
A
A
OE2
O
GLU
HOH
42
1082
2.14
B
1_555
4_575
0.1986
0.1831
0.1839
1.071
28.038
1676
32553
31032
5.12
97.45
0.07
1
0.81
SAD
17.61
1.10
1.30
MLHL
FLAT BULK SOLVENT MODEL
1.071
28.038
89
605
10
0
506
0.007
584
1.242
803
16.151
244
0.086
95
0.005
108
0.2894
0.2743
1.1028
138
2480
12
95.00
0.2425
0.2050
1.1384
136
2498
12
96.00
0.2203
0.1711
1.1791
138
2502
12
96.00
0.1852
0.1666
1.2263
131
2542
12
97.00
0.2193
0.1881
1.2821
141
2540
12
97.00
0.1663
0.1558
1.3497
142
2583
12
97.00
0.1800
0.1532
1.4342
134
2576
12
99.00
0.1693
0.1519
1.5450
139
2614
12
98.00
0.1728
0.1516
1.7004
146
2600
12
99.00
0.1823
0.1707
1.9464
148
2652
12
99.00
0.1550
0.1856
2.4521
147
2677
12
100.00
0.2434
0.2023
28.0472
136
2763
12
98.00
1.07
50.0
4Q2L
32553
31739
3.0
3.0
0.051
1
31.7
7.3
97.5
0.889
1.07
1.11
3.0
3147
1
7.1
95.3
data collection
ADSC
Quantum
phasing
PHASES
refinement
PHENIX
(phenix.refine: 1.8_1069)
data reduction
HKL-2000
data scaling
HKL-2000
Atomic Resolution Structure of the E. coli YajR Transporter YAM Domain
1
N
N
2
N
N
2
N
N
3
N
N
3
N
N
4
N
N
A
ASN
21
A
ASN
24
HELX_P
A
GLU
30
A
GLU
33
1
1
10
A
ASN
56
A
ASN
59
HELX_P
A
GLN
66
A
GLN
69
1
2
11
metalc
2.539
A
A
GLU
13
A
OE2
GLU
16
1_555
A
CD
104
E
CD
CD
1_555
metalc
2.268
A
GLU
43
A
O
GLU
46
1_555
A
CD
104
E
CD
CD
1_555
metalc
2.312
A
HIS
44
A
ND1
HIS
47
1_555
A
CD
103
D
CD
CD
1_555
metalc
2.628
A
ACY
101
B
O
ACY
1_555
A
CD
103
D
CD
CD
1_555
metalc
2.352
A
CD
103
D
CD
CD
1_555
A
HOH
1039
F
O
HOH
1_555
metalc
2.467
A
CD
103
D
CD
CD
1_555
A
HOH
1040
F
O
HOH
1_555
metalc
2.634
A
CD
104
E
CD
CD
1_555
A
HOH
1035
F
O
HOH
1_555
metalc
2.602
A
CD
104
E
CD
CD
1_555
A
HOH
1088
F
O
HOH
1_555
TRANSPORT PROTEIN
Feredoxin Fold, transporter, TRANSPORT PROTEIN
C6EL42_ECOBD
UNP
1
388
C6EL42
MKEPPYVSSLRIEIPADIAANEALKVRLLETEGVKEVLIAEEEHSAYVKIDSKVTNRFEVEQAIRQA
388
454
4Q2L
1
67
C6EL42
A
1
4
70
1
expression tag
GLY
-2
4Q2L
A
C6EL42
UNP
1
1
expression tag
SER
-1
4Q2L
A
C6EL42
UNP
2
1
expression tag
HIS
0
4Q2L
A
C6EL42
UNP
3
3
anti-parallel
anti-parallel
A
VAL
7
A
VAL
10
A
GLU
13
A
GLU
16
A
SER
45
A
SER
48
A
ASP
51
A
ASP
54
A
VAL
34
A
VAL
37
A
ALA
40
A
ALA
43
BINDING SITE FOR RESIDUE ACY A 101
A
ACY
101
Software
7
BINDING SITE FOR RESIDUE ACY A 102
A
ACY
102
Software
4
BINDING SITE FOR RESIDUE CD A 103
A
CD
103
Software
5
BINDING SITE FOR RESIDUE CD A 104
A
CD
104
Software
5
A
GLU
30
A
GLU
33
7
8_475
A
GLU
41
A
GLU
44
7
1_555
A
GLU
42
A
GLU
45
7
1_555
A
HIS
44
A
HIS
47
7
1_555
A
CD
103
D
CD
7
1_555
A
HOH
1051
F
HOH
7
1_555
A
HOH
1074
F
HOH
7
1_555
A
SER
52
A
SER
55
4
1_555
A
LYS
53
A
LYS
56
4
3_655
A
ASN
56
A
ASN
59
4
1_555
A
HOH
1065
F
HOH
4
1_555
A
GLU
30
A
GLU
33
5
8_475
A
HIS
44
A
HIS
47
5
1_555
A
ACY
101
B
ACY
5
1_555
A
HOH
1039
F
HOH
5
1_555
A
HOH
1040
F
HOH
5
1_555
A
GLU
13
A
GLU
16
5
1_555
A
GLU
42
A
GLU
45
5
4_575
A
GLU
43
A
GLU
46
5
1_555
A
HOH
1035
F
HOH
5
1_555
A
HOH
1088
F
HOH
5
1_555
20
C 2 2 21