0.018896
0.010909
0.000000
0.000000
0.021819
0.000000
0.000000
0.000000
0.009776
0.00000
0.00000
0.00000
Filippova, E.V.
Minasov, G.
Shuvalova, L.
Kiryukhina, O.
Cobb, G.
Joachimiak, A.
Anderson, W.F.
Midwest Center for Structural Genomics (MCSG)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
52.922
52.922
102.295
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
Cl -1
35.453
CHLORIDE ION
non-polymer
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
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 Se
196.106
n
SELENOMETHIONINE
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
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
To be Published
0353
Crystal Structure of a Putative Endonuclease-Like Protein (Ngo0050) from Neisseria Gonorrhoeae
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100.0
1
MIRROR
CCD
2009-05-29
SI-111 CHANNEL
SINGLE WAVELENGTH
M
x-ray
1
0.97872
1.0
21-ID-F
APS
0.97872
0.97872
SYNCHROTRON
APS BEAMLINE 21-ID-F
12215.399
Endonuclease-Like Protein
1
man
polymer
35.453
CHLORIDE ION
1
syn
non-polymer
18.015
water
105
nat
water
no
yes
SNA(MSE)SEAEAKLWQHLRAGRLNGYKFRRQQP(MSE)GNYIVDF(MSE)CVTPKLIVEADGGQHAEQAVYDHARTVYL
NSLGFTVLRFWNHEILQQTNDVLAEILRVLQELEKQ
SNAMSEAEAKLWQHLRAGRLNGYKFRRQQPMGNYIVDFMCVTPKLIVEADGGQHAEQAVYDHARTVYLNSLGFTVLRFWN
HEILQQTNDVLAEILRVLQELEKQ
A
apc63439.1
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
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
sample
NGO0050
242231
Neisseria gonorrhoeae FA 1090
511693
Escherichia coli BL21
BL21magic
PLASMID
pMCSG7
1
3.39
63.67
VAPOR DIFFUSION, HANGING DROP
7.0
3M NaCl, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
294
Midwest Center for Structural Genomics
MCSG
PSI, Protein Structure Initiative
software
repository
Initial release
Advisory
Version format compliance
Refinement description
1
0
2009-06-30
1
1
2011-07-13
1
2
2017-11-01
_software.name
Y
RCSB
Y
RCSB
2009-06-09
REL
REL
CL
CHLORIDE ION
HOH
water
CL
1
2
CL
CL
1
A
HOH
2
3
HOH
HOH
2
A
HOH
3
3
HOH
HOH
3
A
HOH
4
3
HOH
HOH
4
A
HOH
5
3
HOH
HOH
5
A
HOH
6
3
HOH
HOH
6
A
HOH
7
3
HOH
HOH
7
A
HOH
8
3
HOH
HOH
8
A
HOH
9
3
HOH
HOH
9
A
HOH
10
3
HOH
HOH
10
A
HOH
11
3
HOH
HOH
11
A
HOH
12
3
HOH
HOH
12
A
HOH
13
3
HOH
HOH
13
A
HOH
14
3
HOH
HOH
14
A
HOH
15
3
HOH
HOH
15
A
HOH
16
3
HOH
HOH
16
A
HOH
17
3
HOH
HOH
17
A
HOH
18
3
HOH
HOH
18
A
HOH
19
3
HOH
HOH
19
A
HOH
20
3
HOH
HOH
20
A
HOH
21
3
HOH
HOH
21
A
HOH
22
3
HOH
HOH
22
A
HOH
23
3
HOH
HOH
23
A
HOH
24
3
HOH
HOH
24
A
HOH
25
3
HOH
HOH
25
A
HOH
26
3
HOH
HOH
127
A
HOH
27
3
HOH
HOH
128
A
HOH
28
3
HOH
HOH
129
A
HOH
29
3
HOH
HOH
130
A
HOH
30
3
HOH
HOH
131
A
HOH
31
3
HOH
HOH
132
A
HOH
32
3
HOH
HOH
133
A
HOH
33
3
HOH
HOH
134
A
HOH
34
3
HOH
HOH
135
A
HOH
35
3
HOH
HOH
136
A
HOH
36
3
HOH
HOH
137
A
HOH
37
3
HOH
HOH
138
A
HOH
38
3
HOH
HOH
139
A
HOH
39
3
HOH
HOH
140
A
HOH
40
3
HOH
HOH
141
A
HOH
41
3
HOH
HOH
142
A
HOH
42
3
HOH
HOH
143
A
HOH
43
3
HOH
HOH
144
A
HOH
44
3
HOH
HOH
145
A
HOH
45
3
HOH
HOH
146
A
HOH
46
3
HOH
HOH
147
A
HOH
47
3
HOH
HOH
148
A
HOH
48
3
HOH
HOH
149
A
HOH
49
3
HOH
HOH
150
A
HOH
50
3
HOH
HOH
151
A
HOH
51
3
HOH
HOH
152
A
HOH
52
3
HOH
HOH
153
A
HOH
53
3
HOH
HOH
154
A
HOH
54
3
HOH
HOH
155
A
HOH
55
3
HOH
HOH
156
A
HOH
56
3
HOH
HOH
157
A
HOH
57
3
HOH
HOH
158
A
HOH
58
3
HOH
HOH
159
A
HOH
59
3
HOH
HOH
160
A
HOH
60
3
HOH
HOH
161
A
HOH
61
3
HOH
HOH
162
A
HOH
62
3
HOH
HOH
163
A
HOH
63
3
HOH
HOH
164
A
HOH
64
3
HOH
HOH
165
A
HOH
65
3
HOH
HOH
166
A
HOH
66
3
HOH
HOH
167
A
HOH
67
3
HOH
HOH
168
A
HOH
68
3
HOH
HOH
169
A
HOH
69
3
HOH
HOH
170
A
HOH
70
3
HOH
HOH
171
A
HOH
71
3
HOH
HOH
172
A
HOH
72
3
HOH
HOH
173
A
HOH
73
3
HOH
HOH
174
A
HOH
74
3
HOH
HOH
175
A
HOH
75
3
HOH
HOH
176
A
HOH
76
3
HOH
HOH
177
A
HOH
77
3
HOH
HOH
178
A
HOH
78
3
HOH
HOH
179
A
HOH
79
3
HOH
HOH
180
A
HOH
80
3
HOH
HOH
181
A
HOH
81
3
HOH
HOH
182
A
HOH
82
3
HOH
HOH
183
A
HOH
83
3
HOH
HOH
184
A
HOH
84
3
HOH
HOH
185
A
HOH
85
3
HOH
HOH
186
A
HOH
86
3
HOH
HOH
187
A
HOH
87
3
HOH
HOH
188
A
HOH
88
3
HOH
HOH
189
A
HOH
89
3
HOH
HOH
190
A
HOH
90
3
HOH
HOH
191
A
HOH
91
3
HOH
HOH
192
A
HOH
92
3
HOH
HOH
193
A
HOH
93
3
HOH
HOH
194
A
HOH
94
3
HOH
HOH
195
A
HOH
95
3
HOH
HOH
196
A
HOH
96
3
HOH
HOH
197
A
HOH
97
3
HOH
HOH
198
A
HOH
98
3
HOH
HOH
199
A
HOH
99
3
HOH
HOH
200
A
HOH
100
3
HOH
HOH
201
A
HOH
101
3
HOH
HOH
202
A
HOH
102
3
HOH
HOH
203
A
HOH
103
3
HOH
HOH
204
A
HOH
104
3
HOH
HOH
205
A
HOH
105
3
HOH
HOH
206
A
HOH
106
3
HOH
HOH
207
A
n
1
-2
A
n
2
-1
A
ALA
0
n
3
ALA
0
A
MSE
26
n
4
MSE
26
A
SER
27
n
5
SER
27
A
GLU
28
n
6
GLU
28
A
ALA
29
n
7
ALA
29
A
GLU
30
n
8
GLU
30
A
ALA
31
n
9
ALA
31
A
LYS
32
n
10
LYS
32
A
LEU
33
n
11
LEU
33
A
TRP
34
n
12
TRP
34
A
GLN
35
n
13
GLN
35
A
HIS
36
n
14
HIS
36
A
LEU
37
n
15
LEU
37
A
ARG
38
n
16
ARG
38
A
ALA
39
n
17
ALA
39
A
GLY
40
n
18
GLY
40
A
ARG
41
n
19
ARG
41
A
LEU
42
n
20
LEU
42
A
ASN
43
n
21
ASN
43
A
GLY
44
n
22
GLY
44
A
TYR
45
n
23
TYR
45
A
LYS
46
n
24
LYS
46
A
PHE
47
n
25
PHE
47
A
ARG
48
n
26
ARG
48
A
ARG
49
n
27
ARG
49
A
GLN
50
n
28
GLN
50
A
GLN
51
n
29
GLN
51
A
PRO
52
n
30
PRO
52
A
MSE
53
n
31
MSE
53
A
GLY
54
n
32
GLY
54
A
ASN
55
n
33
ASN
55
A
TYR
56
n
34
TYR
56
A
ILE
57
n
35
ILE
57
A
VAL
58
n
36
VAL
58
A
ASP
59
n
37
ASP
59
A
PHE
60
n
38
PHE
60
A
MSE
61
n
39
MSE
61
A
CYS
62
n
40
CYS
62
A
VAL
63
n
41
VAL
63
A
THR
64
n
42
THR
64
A
PRO
65
n
43
PRO
65
A
LYS
66
n
44
LYS
66
A
LEU
67
n
45
LEU
67
A
ILE
68
n
46
ILE
68
A
VAL
69
n
47
VAL
69
A
GLU
70
n
48
GLU
70
A
ALA
71
n
49
ALA
71
A
ASP
72
n
50
ASP
72
A
GLY
73
n
51
GLY
73
A
n
52
74
A
n
53
75
A
n
54
76
A
n
55
77
A
n
56
78
A
n
57
79
A
n
58
80
A
VAL
81
n
59
VAL
81
A
TYR
82
n
60
TYR
82
A
ASP
83
n
61
ASP
83
A
HIS
84
n
62
HIS
84
A
ALA
85
n
63
ALA
85
A
ARG
86
n
64
ARG
86
A
THR
87
n
65
THR
87
A
VAL
88
n
66
VAL
88
A
TYR
89
n
67
TYR
89
A
LEU
90
n
68
LEU
90
A
ASN
91
n
69
ASN
91
A
SER
92
n
70
SER
92
A
LEU
93
n
71
LEU
93
A
GLY
94
n
72
GLY
94
A
PHE
95
n
73
PHE
95
A
THR
96
n
74
THR
96
A
VAL
97
n
75
VAL
97
A
LEU
98
n
76
LEU
98
A
ARG
99
n
77
ARG
99
A
PHE
100
n
78
PHE
100
A
TRP
101
n
79
TRP
101
A
ASN
102
n
80
ASN
102
A
HIS
103
n
81
HIS
103
A
GLU
104
n
82
GLU
104
A
ILE
105
n
83
ILE
105
A
LEU
106
n
84
LEU
106
A
GLN
107
n
85
GLN
107
A
GLN
108
n
86
GLN
108
A
THR
109
n
87
THR
109
A
ASN
110
n
88
ASN
110
A
ASP
111
n
89
ASP
111
A
VAL
112
n
90
VAL
112
A
LEU
113
n
91
LEU
113
A
ALA
114
n
92
ALA
114
A
GLU
115
n
93
GLU
115
A
ILE
116
n
94
ILE
116
A
LEU
117
n
95
LEU
117
A
ARG
118
n
96
ARG
118
A
VAL
119
n
97
VAL
119
A
LEU
120
n
98
LEU
120
A
GLN
121
n
99
GLN
121
A
GLU
122
n
100
GLU
122
A
LEU
123
n
101
LEU
123
A
GLU
124
n
102
GLU
124
A
LYS
125
n
103
LYS
125
A
n
104
126
A
2.8971
0.5420
0.9626
0.9887
0.4558
1.4877
-0.0131
0.1571
-0.0196
-0.0458
0.0904
0.0156
-0.0181
0.0068
-0.0773
0.0517
0.0085
0.0086
0.0852
0.0165
0.0103
refined
34.4501
22.4862
20.4432
X-RAY DIFFRACTION
A
26
A
125
X-RAY DIFFRACTION
1
author_and_software_defined_assembly
PISA
1
monomeric
A
MSE
26
SELENOMETHIONINE
A
MSE
4
MET
A
MSE
53
SELENOMETHIONINE
A
MSE
31
MET
A
MSE
61
SELENOMETHIONINE
A
MSE
39
MET
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
N
MSE
53
A
N
MSE
31
A
O
TYR
56
A
O
TYR
34
A
N
CYS
62
A
N
CYS
40
A
O
LEU
67
A
O
LEU
45
A
N
ASP
72
A
N
ASP
50
A
O
PHE
100
A
O
PHE
78
1
A
SER
-2
A
SER
1
1
Y
1
A
ASN
-1
A
ASN
2
1
Y
1
A
GLY
74
A
GLY
52
1
Y
1
A
GLN
75
A
GLN
53
1
Y
1
A
HIS
76
A
HIS
54
1
Y
1
A
ALA
77
A
ALA
55
1
Y
1
A
GLU
78
A
GLU
56
1
Y
1
A
GLN
79
A
GLN
57
1
Y
1
A
ALA
80
A
ALA
58
1
Y
1
A
GLN
126
A
GLN
104
1
Y
19.925
1.65
0.82
0.00
1.65
0.00
-2.47
0.957
0.943
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.22600
0.18316
0.18521
1.95
22.33
604
12588
11984
4.8
99.83
5.694
0.077
RANDOM
LIKELY RESIDUAL
1
THROUGHOUT
SAD
0.117
0.122
0.80
0.80
1.20
MAXIMUM LIKELIHOOD
MASK
1.95
22.33
105
881
1
0
775
0.019
0.022
790
0.001
0.020
539
1.615
1.941
1066
0.901
3.000
1301
5.733
5.000
92
28.800
23.571
42
12.223
15.000
141
12.846
15.000
7
0.098
0.200
117
0.007
0.020
867
0.001
0.020
170
1.087
1.500
465
0.314
1.500
190
1.997
2.000
746
3.529
3.000
325
5.930
4.500
320
0.265
0.190
2.001
37
839
20
98.65
1.950
22.330
3HRL
23330
23330
-3.000
0.07000
0.07000
1
21.7120
5.800
99.9
0.35300
1.95
1.98
5.200
0.35300
1
5.80
98.7
data collection
Blu-Ice
Max
phasing
HKL-3000
phasing
MLPHARE
model building
DM
phasing
SHELXD
model building
ARP/wARP
model building
Coot
refinement
REFMAC
5.5.0051
data reduction
HKL-2000
data scaling
HKL-2000
phasing
DM
Endonuclease-Like Protein
Crystal structure of a putative endonuclease-like protein (ngo0050) from neisseria gonorrhoeae
1
N
N
2
N
N
3
N
N
A
SER
27
A
SER
5
HELX_P
A
ARG
38
A
ARG
16
1
1
12
A
ALA
39
A
ALA
17
HELX_P
A
ARG
41
A
ARG
19
5
2
3
A
ASP
83
A
ASP
61
HELX_P
A
LEU
93
A
LEU
71
1
3
11
A
ASN
102
A
ASN
80
HELX_P
A
GLN
108
A
GLN
86
1
4
7
A
GLN
108
A
GLN
86
HELX_P
A
LYS
125
A
LYS
103
1
5
18
covale
1.332
A
ALA
0
A
C
ALA
3
1_555
A
MSE
26
A
N
MSE
4
1_555
covale
1.327
A
MSE
26
A
C
MSE
4
1_555
A
SER
27
A
N
SER
5
1_555
covale
1.325
A
PRO
52
A
C
PRO
30
1_555
A
MSE
53
A
N
MSE
31
1_555
covale
1.322
A
MSE
53
A
C
MSE
31
1_555
A
GLY
54
A
N
GLY
32
1_555
covale
1.330
A
PHE
60
A
C
PHE
38
1_555
A
MSE
61
A
N
MSE
39
1_555
covale
1.323
A
MSE
61
A
C
MSE
39
1_555
A
CYS
62
A
N
CYS
40
1_555
structural genomics, unknown function
STRUCTURAL GENOMICS; ENDONUCLEASE; NEISSERIA GONORRHOEAE, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, structural genomics, unknown function
A
THR
64
A
THR
42
1
A
PRO
65
A
PRO
43
-3.69
Q5FAH0_NEIG1
UNP
1
27
Q5FAH0
SEAEAKLWQHLRAGRLNGYKFRRQQPMGNYIVDFMCVTPKLIVEADGGQHAEQAVYDHARTVYLNSLGFTVLRFWNHEIL
QQTNDVLAEILRVLQELEKQ
27
126
3HRL
27
126
Q5FAH0
A
1
5
104
1
expression tag
SER
-2
3HRL
A
Q5FAH0
UNP
1
1
expression tag
ASN
-1
3HRL
A
Q5FAH0
UNP
2
1
expression tag
ALA
0
3HRL
A
Q5FAH0
UNP
3
1
expression tag
MSE
26
3HRL
A
Q5FAH0
UNP
4
4
anti-parallel
anti-parallel
parallel
A
PHE
47
A
PHE
25
A
MSE
53
A
MSE
31
A
TYR
56
A
TYR
34
A
CYS
62
A
CYS
40
A
LEU
67
A
LEU
45
A
ASP
72
A
ASP
50
A
THR
96
A
THR
74
A
TRP
101
A
TRP
79
BINDING SITE FOR RESIDUE CL A 1
Software
4
A
TYR
56
A
TYR
34
4
1_555
A
ILE
57
A
ILE
35
4
1_555
A
ARG
86
A
ARG
64
4
1_555
A
HOH
146
C
HOH
4
1_555
154
P 32 2 1