0.012887
0.007440
0.000000
0.000000
0.014881
0.000000
0.000000
0.000000
0.004378
0.00000
0.00000
0.00000
Sampathkumar, P.
Almo, S.C.
New York Structural Genomics Research Consortium (NYSGRC)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
120.00
77.598
77.598
228.425
C5 H5 N5
135.127
ADENINE
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
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C2 H6 O2
62.068
1,2-ETHANEDIOL
ETHYLENE GLYCOL
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 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 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Sulfurimonas denitrificans DSM 1251
100
1
MIRRORS
CCD
2013-02-15
ADSC QUANTUM 315r
Si(111)
SINGLE WAVELENGTH
M
x-ray
1
0.97910
1.0
X29A
NSLS
0.97910
SYNCHROTRON
NSLS BEAMLINE X29A
28637.805
Methylthioadenosine nucleosidase
3.2.2.16
1
man
polymer
62.068
1,2-ETHANEDIOL
4
syn
non-polymer
135.127
ADENINE
1
syn
non-polymer
18.015
water
139
nat
water
no
yes
(MSE)HHHHHHSSGVDLGTENLYFQS(MSE)KIAI(MSE)GA(MSE)PEEISPILEKIGSYKSTSYAGNKYYEATYQGVE
LVIAYSKIGKVFSALSAAT(MSE)IEHFGATKLLFSGVAGAISTNLKVGDLIVATKLSQHDLDITAFGHPYGYVPEGSVF
VEADKD(MSE)IELSKKVALE(MSE)GKSVQEGIIATGDQFVANEERKNWIGTTFGADALE(MSE)EGGSVGVVCNALNI
PFFILRSISDAAD(MSE)DASFSFDEFLESSAKESAEFI(MSE)K(MSE)VDELVALPLQDIK
MHHHHHHSSGVDLGTENLYFQSMKIAIMGAMPEEISPILEKIGSYKSTSYAGNKYYEATYQGVELVIAYSKIGKVFSALS
AATMIEHFGATKLLFSGVAGAISTNLKVGDLIVATKLSQHDLDITAFGHPYGYVPEGSVFVEADKDMIELSKKVALEMGK
SVQEGIIATGDQFVANEERKNWIGTTFGADALEMEGGSVGVVCNALNIPFFILRSISDAADMDASFSFDEFLESSAKESA
EFIMKMVDELVALPLQDIK
A
NYSGRC-029304
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
DSM 1251
sample
Suden_1392
326298
Sulfurimonas denitrificans
469008
Escherichia coli
BL21(DE3) CodonPlus RIL
Plasmid
pSGC-His
1
3.54
65.26
VAPOR DIFFUSION, SITTING DROP
4.6
Protein (20mM HEPES pH7.5, 150mM NaCl, 5% glycerol, and 5mM DTT); Reservoir (MCSG3 #84; 0.1 M Sodium Acetate:HCl pH 4.6,
2.0 M Sodium Formate ); Cryoprotection (33% Ethylene glycol), VAPOR DIFFUSION, SITTING DROP, temperature 298K
298
New York Structural Genomics Research Consortium
NYSGRC
PSI:Biology
software
repository
Initial release
Structure summary
Refinement description
1
0
2013-05-08
1
1
2013-11-27
1
2
2017-11-15
_software.classification
_software.name
Y
RCSB
Y
RCSB
2013-03-27
REL
REL
EDO
1,2-ETHANEDIOL
ADE
ADENINE
HOH
water
EDO
1
2
EDO
EDO
301
A
EDO
2
2
EDO
EDO
302
A
EDO
3
2
EDO
EDO
303
A
EDO
4
2
EDO
EDO
304
A
ADE
1
3
ADE
ADE
305
A
HOH
1
4
HOH
HOH
401
A
HOH
2
4
HOH
HOH
402
A
HOH
3
4
HOH
HOH
403
A
HOH
4
4
HOH
HOH
404
A
HOH
5
4
HOH
HOH
405
A
HOH
6
4
HOH
HOH
406
A
HOH
7
4
HOH
HOH
407
A
HOH
8
4
HOH
HOH
408
A
HOH
9
4
HOH
HOH
409
A
HOH
10
4
HOH
HOH
410
A
HOH
11
4
HOH
HOH
411
A
HOH
12
4
HOH
HOH
412
A
HOH
13
4
HOH
HOH
413
A
HOH
14
4
HOH
HOH
414
A
HOH
15
4
HOH
HOH
415
A
HOH
16
4
HOH
HOH
416
A
HOH
17
4
HOH
HOH
417
A
HOH
18
4
HOH
HOH
418
A
HOH
19
4
HOH
HOH
419
A
HOH
20
4
HOH
HOH
420
A
HOH
21
4
HOH
HOH
421
A
HOH
22
4
HOH
HOH
422
A
HOH
23
4
HOH
HOH
423
A
HOH
24
4
HOH
HOH
424
A
HOH
25
4
HOH
HOH
425
A
HOH
26
4
HOH
HOH
426
A
HOH
27
4
HOH
HOH
427
A
HOH
28
4
HOH
HOH
428
A
HOH
29
4
HOH
HOH
429
A
HOH
30
4
HOH
HOH
430
A
HOH
31
4
HOH
HOH
431
A
HOH
32
4
HOH
HOH
432
A
HOH
33
4
HOH
HOH
433
A
HOH
34
4
HOH
HOH
434
A
HOH
35
4
HOH
HOH
435
A
HOH
36
4
HOH
HOH
436
A
HOH
37
4
HOH
HOH
437
A
HOH
38
4
HOH
HOH
438
A
HOH
39
4
HOH
HOH
439
A
HOH
40
4
HOH
HOH
440
A
HOH
41
4
HOH
HOH
441
A
HOH
42
4
HOH
HOH
442
A
HOH
43
4
HOH
HOH
443
A
HOH
44
4
HOH
HOH
444
A
HOH
45
4
HOH
HOH
445
A
HOH
46
4
HOH
HOH
446
A
HOH
47
4
HOH
HOH
447
A
HOH
48
4
HOH
HOH
448
A
HOH
49
4
HOH
HOH
449
A
HOH
50
4
HOH
HOH
450
A
HOH
51
4
HOH
HOH
451
A
HOH
52
4
HOH
HOH
452
A
HOH
53
4
HOH
HOH
453
A
HOH
54
4
HOH
HOH
454
A
HOH
55
4
HOH
HOH
455
A
HOH
56
4
HOH
HOH
456
A
HOH
57
4
HOH
HOH
457
A
HOH
58
4
HOH
HOH
458
A
HOH
59
4
HOH
HOH
459
A
HOH
60
4
HOH
HOH
460
A
HOH
61
4
HOH
HOH
461
A
HOH
62
4
HOH
HOH
462
A
HOH
63
4
HOH
HOH
463
A
HOH
64
4
HOH
HOH
464
A
HOH
65
4
HOH
HOH
465
A
HOH
66
4
HOH
HOH
466
A
HOH
67
4
HOH
HOH
467
A
HOH
68
4
HOH
HOH
468
A
HOH
69
4
HOH
HOH
469
A
HOH
70
4
HOH
HOH
470
A
HOH
71
4
HOH
HOH
471
A
HOH
72
4
HOH
HOH
472
A
HOH
73
4
HOH
HOH
473
A
HOH
74
4
HOH
HOH
474
A
HOH
75
4
HOH
HOH
475
A
HOH
76
4
HOH
HOH
476
A
HOH
77
4
HOH
HOH
477
A
HOH
78
4
HOH
HOH
478
A
HOH
79
4
HOH
HOH
479
A
HOH
80
4
HOH
HOH
480
A
HOH
81
4
HOH
HOH
481
A
HOH
82
4
HOH
HOH
482
A
HOH
83
4
HOH
HOH
483
A
HOH
84
4
HOH
HOH
484
A
HOH
85
4
HOH
HOH
485
A
HOH
86
4
HOH
HOH
486
A
HOH
87
4
HOH
HOH
487
A
HOH
88
4
HOH
HOH
488
A
HOH
89
4
HOH
HOH
489
A
HOH
90
4
HOH
HOH
490
A
HOH
91
4
HOH
HOH
491
A
HOH
92
4
HOH
HOH
492
A
HOH
93
4
HOH
HOH
493
A
HOH
94
4
HOH
HOH
494
A
HOH
95
4
HOH
HOH
495
A
HOH
96
4
HOH
HOH
496
A
HOH
97
4
HOH
HOH
497
A
HOH
98
4
HOH
HOH
498
A
HOH
99
4
HOH
HOH
499
A
HOH
100
4
HOH
HOH
500
A
HOH
101
4
HOH
HOH
501
A
HOH
102
4
HOH
HOH
502
A
HOH
103
4
HOH
HOH
503
A
HOH
104
4
HOH
HOH
504
A
HOH
105
4
HOH
HOH
505
A
HOH
106
4
HOH
HOH
506
A
HOH
107
4
HOH
HOH
507
A
HOH
108
4
HOH
HOH
508
A
HOH
109
4
HOH
HOH
509
A
HOH
110
4
HOH
HOH
510
A
HOH
111
4
HOH
HOH
511
A
HOH
112
4
HOH
HOH
512
A
HOH
113
4
HOH
HOH
513
A
HOH
114
4
HOH
HOH
514
A
HOH
115
4
HOH
HOH
515
A
HOH
116
4
HOH
HOH
516
A
HOH
117
4
HOH
HOH
517
A
HOH
118
4
HOH
HOH
518
A
HOH
119
4
HOH
HOH
519
A
HOH
120
4
HOH
HOH
520
A
HOH
121
4
HOH
HOH
521
A
HOH
122
4
HOH
HOH
522
A
HOH
123
4
HOH
HOH
523
A
HOH
124
4
HOH
HOH
524
A
HOH
125
4
HOH
HOH
525
A
HOH
126
4
HOH
HOH
526
A
HOH
127
4
HOH
HOH
527
A
HOH
128
4
HOH
HOH
528
A
HOH
129
4
HOH
HOH
529
A
HOH
130
4
HOH
HOH
530
A
HOH
131
4
HOH
HOH
531
A
HOH
132
4
HOH
HOH
532
A
HOH
133
4
HOH
HOH
533
A
HOH
134
4
HOH
HOH
534
A
HOH
135
4
HOH
HOH
535
A
HOH
136
4
HOH
HOH
536
A
HOH
137
4
HOH
HOH
537
A
HOH
138
4
HOH
HOH
538
A
HOH
139
4
HOH
HOH
539
A
n
1
-21
A
n
2
-20
A
n
3
-19
A
n
4
-18
A
n
5
-17
A
n
6
-16
A
n
7
-15
A
n
8
-14
A
n
9
-13
A
GLY
-12
n
10
GLY
-12
A
VAL
-11
n
11
VAL
-11
A
ASP
-10
n
12
ASP
-10
A
LEU
-9
n
13
LEU
-9
A
GLY
-8
n
14
GLY
-8
A
THR
-7
n
15
THR
-7
A
GLU
-6
n
16
GLU
-6
A
ASN
-5
n
17
ASN
-5
A
LEU
-4
n
18
LEU
-4
A
TYR
-3
n
19
TYR
-3
A
PHE
-2
n
20
PHE
-2
A
GLN
-1
n
21
GLN
-1
A
SER
0
n
22
SER
0
A
MSE
1
n
23
MSE
1
A
LYS
2
n
24
LYS
2
A
ILE
3
n
25
ILE
3
A
ALA
4
n
26
ALA
4
A
ILE
5
n
27
ILE
5
A
MSE
6
n
28
MSE
6
A
GLY
7
n
29
GLY
7
A
ALA
8
n
30
ALA
8
A
MSE
9
n
31
MSE
9
A
PRO
10
n
32
PRO
10
A
GLU
11
n
33
GLU
11
A
GLU
12
n
34
GLU
12
A
ILE
13
n
35
ILE
13
A
SER
14
n
36
SER
14
A
PRO
15
n
37
PRO
15
A
ILE
16
n
38
ILE
16
A
LEU
17
n
39
LEU
17
A
GLU
18
n
40
GLU
18
A
LYS
19
n
41
LYS
19
A
ILE
20
n
42
ILE
20
A
GLY
21
n
43
GLY
21
A
SER
22
n
44
SER
22
A
TYR
23
n
45
TYR
23
A
LYS
24
n
46
LYS
24
A
SER
25
n
47
SER
25
A
THR
26
n
48
THR
26
A
SER
27
n
49
SER
27
A
TYR
28
n
50
TYR
28
A
ALA
29
n
51
ALA
29
A
GLY
30
n
52
GLY
30
A
ASN
31
n
53
ASN
31
A
LYS
32
n
54
LYS
32
A
TYR
33
n
55
TYR
33
A
TYR
34
n
56
TYR
34
A
GLU
35
n
57
GLU
35
A
ALA
36
n
58
ALA
36
A
THR
37
n
59
THR
37
A
TYR
38
n
60
TYR
38
A
GLN
39
n
61
GLN
39
A
GLY
40
n
62
GLY
40
A
VAL
41
n
63
VAL
41
A
GLU
42
n
64
GLU
42
A
LEU
43
n
65
LEU
43
A
VAL
44
n
66
VAL
44
A
ILE
45
n
67
ILE
45
A
ALA
46
n
68
ALA
46
A
TYR
47
n
69
TYR
47
A
SER
48
n
70
SER
48
A
LYS
49
n
71
LYS
49
A
ILE
50
n
72
ILE
50
A
GLY
51
n
73
GLY
51
A
LYS
52
n
74
LYS
52
A
VAL
53
n
75
VAL
53
A
PHE
54
n
76
PHE
54
A
SER
55
n
77
SER
55
A
ALA
56
n
78
ALA
56
A
LEU
57
n
79
LEU
57
A
SER
58
n
80
SER
58
A
ALA
59
n
81
ALA
59
A
ALA
60
n
82
ALA
60
A
THR
61
n
83
THR
61
A
MSE
62
n
84
MSE
62
A
ILE
63
n
85
ILE
63
A
GLU
64
n
86
GLU
64
A
HIS
65
n
87
HIS
65
A
PHE
66
n
88
PHE
66
A
GLY
67
n
89
GLY
67
A
ALA
68
n
90
ALA
68
A
THR
69
n
91
THR
69
A
LYS
70
n
92
LYS
70
A
LEU
71
n
93
LEU
71
A
LEU
72
n
94
LEU
72
A
PHE
73
n
95
PHE
73
A
SER
74
n
96
SER
74
A
GLY
75
n
97
GLY
75
A
VAL
76
n
98
VAL
76
A
ALA
77
n
99
ALA
77
A
GLY
78
n
100
GLY
78
A
ALA
79
n
101
ALA
79
A
ILE
80
n
102
ILE
80
A
SER
81
n
103
SER
81
A
THR
82
n
104
THR
82
A
ASN
83
n
105
ASN
83
A
LEU
84
n
106
LEU
84
A
LYS
85
n
107
LYS
85
A
VAL
86
n
108
VAL
86
A
GLY
87
n
109
GLY
87
A
ASP
88
n
110
ASP
88
A
LEU
89
n
111
LEU
89
A
ILE
90
n
112
ILE
90
A
VAL
91
n
113
VAL
91
A
ALA
92
n
114
ALA
92
A
THR
93
n
115
THR
93
A
LYS
94
n
116
LYS
94
A
LEU
95
n
117
LEU
95
A
SER
96
n
118
SER
96
A
GLN
97
n
119
GLN
97
A
HIS
98
n
120
HIS
98
A
ASP
99
n
121
ASP
99
A
LEU
100
n
122
LEU
100
A
ASP
101
n
123
ASP
101
A
ILE
102
n
124
ILE
102
A
THR
103
n
125
THR
103
A
ALA
104
n
126
ALA
104
A
PHE
105
n
127
PHE
105
A
GLY
106
n
128
GLY
106
A
HIS
107
n
129
HIS
107
A
PRO
108
n
130
PRO
108
A
TYR
109
n
131
TYR
109
A
GLY
110
n
132
GLY
110
A
TYR
111
n
133
TYR
111
A
VAL
112
n
134
VAL
112
A
PRO
113
n
135
PRO
113
A
GLU
114
n
136
GLU
114
A
GLY
115
n
137
GLY
115
A
SER
116
n
138
SER
116
A
VAL
117
n
139
VAL
117
A
PHE
118
n
140
PHE
118
A
VAL
119
n
141
VAL
119
A
GLU
120
n
142
GLU
120
A
ALA
121
n
143
ALA
121
A
ASP
122
n
144
ASP
122
A
LYS
123
n
145
LYS
123
A
ASP
124
n
146
ASP
124
A
MSE
125
n
147
MSE
125
A
ILE
126
n
148
ILE
126
A
GLU
127
n
149
GLU
127
A
LEU
128
n
150
LEU
128
A
SER
129
n
151
SER
129
A
LYS
130
n
152
LYS
130
A
LYS
131
n
153
LYS
131
A
VAL
132
n
154
VAL
132
A
ALA
133
n
155
ALA
133
A
LEU
134
n
156
LEU
134
A
GLU
135
n
157
GLU
135
A
MSE
136
n
158
MSE
136
A
GLY
137
n
159
GLY
137
A
LYS
138
n
160
LYS
138
A
SER
139
n
161
SER
139
A
VAL
140
n
162
VAL
140
A
GLN
141
n
163
GLN
141
A
GLU
142
n
164
GLU
142
A
GLY
143
n
165
GLY
143
A
ILE
144
n
166
ILE
144
A
ILE
145
n
167
ILE
145
A
ALA
146
n
168
ALA
146
A
THR
147
n
169
THR
147
A
GLY
148
n
170
GLY
148
A
ASP
149
n
171
ASP
149
A
GLN
150
n
172
GLN
150
A
PHE
151
n
173
PHE
151
A
VAL
152
n
174
VAL
152
A
ALA
153
n
175
ALA
153
A
ASN
154
n
176
ASN
154
A
GLU
155
n
177
GLU
155
A
GLU
156
n
178
GLU
156
A
ARG
157
n
179
ARG
157
A
LYS
158
n
180
LYS
158
A
ASN
159
n
181
ASN
159
A
TRP
160
n
182
TRP
160
A
ILE
161
n
183
ILE
161
A
GLY
162
n
184
GLY
162
A
THR
163
n
185
THR
163
A
THR
164
n
186
THR
164
A
PHE
165
n
187
PHE
165
A
GLY
166
n
188
GLY
166
A
ALA
167
n
189
ALA
167
A
ASP
168
n
190
ASP
168
A
ALA
169
n
191
ALA
169
A
LEU
170
n
192
LEU
170
A
GLU
171
n
193
GLU
171
A
MSE
172
n
194
MSE
172
A
GLU
173
n
195
GLU
173
A
GLY
174
n
196
GLY
174
A
GLY
175
n
197
GLY
175
A
SER
176
n
198
SER
176
A
VAL
177
n
199
VAL
177
A
GLY
178
n
200
GLY
178
A
VAL
179
n
201
VAL
179
A
VAL
180
n
202
VAL
180
A
CYS
181
n
203
CYS
181
A
ASN
182
n
204
ASN
182
A
ALA
183
n
205
ALA
183
A
LEU
184
n
206
LEU
184
A
ASN
185
n
207
ASN
185
A
ILE
186
n
208
ILE
186
A
PRO
187
n
209
PRO
187
A
PHE
188
n
210
PHE
188
A
PHE
189
n
211
PHE
189
A
ILE
190
n
212
ILE
190
A
LEU
191
n
213
LEU
191
A
ARG
192
n
214
ARG
192
A
SER
193
n
215
SER
193
A
ILE
194
n
216
ILE
194
A
SER
195
n
217
SER
195
A
ASP
196
n
218
ASP
196
A
ALA
197
n
219
ALA
197
A
ALA
198
n
220
ALA
198
A
ASP
199
n
221
ASP
199
A
MSE
200
n
222
MSE
200
A
ASP
201
n
223
ASP
201
A
ALA
202
n
224
ALA
202
A
SER
203
n
225
SER
203
A
PHE
204
n
226
PHE
204
A
SER
205
n
227
SER
205
A
PHE
206
n
228
PHE
206
A
ASP
207
n
229
ASP
207
A
GLU
208
n
230
GLU
208
A
PHE
209
n
231
PHE
209
A
LEU
210
n
232
LEU
210
A
GLU
211
n
233
GLU
211
A
SER
212
n
234
SER
212
A
SER
213
n
235
SER
213
A
ALA
214
n
236
ALA
214
A
LYS
215
n
237
LYS
215
A
GLU
216
n
238
GLU
216
A
SER
217
n
239
SER
217
A
ALA
218
n
240
ALA
218
A
GLU
219
n
241
GLU
219
A
PHE
220
n
242
PHE
220
A
ILE
221
n
243
ILE
221
A
MSE
222
n
244
MSE
222
A
LYS
223
n
245
LYS
223
A
MSE
224
n
246
MSE
224
A
VAL
225
n
247
VAL
225
A
ASP
226
n
248
ASP
226
A
GLU
227
n
249
GLU
227
A
LEU
228
n
250
LEU
228
A
VAL
229
n
251
VAL
229
A
ALA
230
n
252
ALA
230
A
LEU
231
n
253
LEU
231
A
PRO
232
n
254
PRO
232
A
n
255
233
A
n
256
234
A
n
257
235
A
n
258
236
A
n
259
237
A
author_and_software_defined_assembly
PISA
2
dimeric
5210
0
19920
A
MSE
1
SELENOMETHIONINE
A
MSE
23
MET
A
MSE
6
SELENOMETHIONINE
A
MSE
28
MET
A
MSE
9
SELENOMETHIONINE
A
MSE
31
MET
A
MSE
62
SELENOMETHIONINE
A
MSE
84
MET
A
MSE
125
SELENOMETHIONINE
A
MSE
147
MET
A
MSE
136
SELENOMETHIONINE
A
MSE
158
MET
A
MSE
172
SELENOMETHIONINE
A
MSE
194
MET
A
MSE
200
SELENOMETHIONINE
A
MSE
222
MET
A
MSE
222
SELENOMETHIONINE
A
MSE
244
MET
A
MSE
224
SELENOMETHIONINE
A
MSE
246
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
0.5000000000
-0.8660254038
0.0000000000
-0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
10_665
-y+1,-x+1,-z+1/6
crystal symmetry operation
38.7990000000
67.2018392829
38.0708333333
A
N
THR
26
A
N
THR
48
A
O
TYR
33
A
O
TYR
55
A
N
TYR
34
A
N
TYR
56
A
O
ILE
45
A
O
ILE
67
A
O
VAL
44
A
O
VAL
66
A
N
ILE
5
A
N
ILE
27
A
N
ALA
4
A
N
ALA
26
A
O
LEU
72
A
O
LEU
94
A
N
GLY
78
A
N
GLY
100
A
O
LEU
170
A
O
LEU
192
A
O
ALA
169
A
O
ALA
191
A
N
ALA
146
A
N
ALA
168
A
O
THR
147
A
O
THR
169
A
N
SER
96
A
N
SER
118
A
N
LEU
95
A
N
LEU
117
A
O
VAL
119
A
O
VAL
141
A
N
THR
26
A
N
THR
48
A
O
TYR
33
A
O
TYR
55
A
N
TYR
34
A
N
TYR
56
A
O
ILE
45
A
O
ILE
67
A
O
VAL
44
A
O
VAL
66
A
N
ILE
5
A
N
ILE
27
A
N
ALA
4
A
N
ALA
26
A
O
LEU
72
A
O
LEU
94
A
N
ALA
77
A
N
ALA
99
A
O
SER
195
A
O
SER
217
A
O
ARG
192
A
O
ARG
214
A
N
ILE
90
A
N
ILE
112
A
N
LEU
95
A
N
LEU
117
A
O
VAL
119
A
O
VAL
141
1
A
HOH
457
G
HOH
1
A
MSE
-21
A
MSE
1
1
Y
1
A
HIS
-20
A
HIS
2
1
Y
1
A
HIS
-19
A
HIS
3
1
Y
1
A
HIS
-18
A
HIS
4
1
Y
1
A
HIS
-17
A
HIS
5
1
Y
1
A
HIS
-16
A
HIS
6
1
Y
1
A
HIS
-15
A
HIS
7
1
Y
1
A
SER
-14
A
SER
8
1
Y
1
A
SER
-13
A
SER
9
1
Y
1
A
LEU
233
A
LEU
255
1
Y
1
A
GLN
234
A
GLN
256
1
Y
1
A
ASP
235
A
ASP
257
1
Y
1
A
ILE
236
A
ILE
258
1
Y
1
A
LYS
237
A
LYS
259
1
Y
1
A
LYS
49
87.62
163.04
1
A
ASP
149
-87.28
33.58
1
A
ASN
154
-162.96
114.66
1
A
GLU
173
-138.35
-30.75
1
A
ASP
199
-122.90
-161.65
113.730
38.1574
20.880
0.2600
0.2600
0.0000
0.2600
0.0000
-0.8300
0.9600
0.9570
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY. AUTHORS NOTE AN ELECTRON DENSITY FEATURE JUST BELOW ADENINE, WHICH COULD NOT BE SATISFACTORILY EXPLAINED WITH BUFFER OR CRYSTALLIZATION COMPONENTS.
0.1929
0.1775
0.1783
2.0500
43.5500
1314
26403
5.0000
99.8600
1.000
0.500
2.9870
0.0810
RANDOM
1
THROUGHOUT
0.000
SAD
0.1290
0.1150
0.8000
0.8000
1.4000
MAXIMUM LIKELIHOOD
BABINET MODEL WITH MASK
2.0500
43.5500
139
2016
26
0
1851
0.009
0.019
1941
0.001
0.020
1860
1.285
1.998
2620
0.718
3.000
4311
5.912
5.000
256
32.045
25.921
76
12.816
15.000
307
12.282
15.000
2
0.074
0.200
297
0.005
0.020
2188
0.001
0.020
407
0.2570
0.2250
2.1050
85
1797
1882
1797
20
98.9000
33.0
2.05
50.00
4JWT
26487
0
0
0.109
1
26.75
22.8
99.9
0.738
2.05
2.09
5.42
1283
1
23.1
100.0
refinement
Garib N. Murshudov
garib@ysbl.york.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/refmac5.html
REFMAC
program
5.7.0029
data extraction
PDB
deposit@deposit.rcsb.org
April 22, 2011
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.11
data collection
CBASS
data reduction
HKL-3000
data scaling
SCALEPACK
phasing
SHELX
C
phasing
SHELXD
model building
SHELXE
Methylthioadenosine nucleosidase (E.C.3.2.2.16)
Crystal structure of a putative 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Sulfurimonas denitrificans DSM 1251 (Target NYSGRC-029304 )
1
N
N
2
N
N
2
N
N
2
N
N
2
N
N
3
N
N
4
N
N
A
THR
-7
A
THR
15
HELX_P
A
TYR
-3
A
TYR
19
5
1
5
A
MSE
9
A
MSE
31
HELX_P
A
GLY
21
A
GLY
43
1
2
13
A
GLY
51
A
GLY
73
HELX_P
A
HIS
65
A
HIS
87
1
3
15
A
ILE
102
A
ILE
124
HELX_P
A
GLY
106
A
GLY
128
5
4
5
A
ASP
122
A
ASP
144
HELX_P
A
GLY
137
A
GLY
159
1
5
16
A
ASN
154
A
ASN
176
HELX_P
A
GLY
166
A
GLY
188
1
6
13
A
GLU
173
A
GLU
195
HELX_P
A
LEU
184
A
LEU
206
1
7
12
A
ASP
201
A
ASP
223
HELX_P
A
LEU
231
A
LEU
253
1
8
31
covale
1.334
A
SER
0
A
C
SER
22
1_555
A
MSE
1
A
N
MSE
23
1_555
covale
1.328
A
MSE
1
A
C
MSE
23
1_555
A
LYS
2
A
N
LYS
24
1_555
covale
1.322
A
ILE
5
A
C
ILE
27
1_555
A
MSE
6
A
N
MSE
28
1_555
covale
1.326
A
MSE
6
A
C
MSE
28
1_555
A
GLY
7
A
N
GLY
29
1_555
covale
1.337
A
ALA
8
A
C
ALA
30
1_555
A
MSE
9
A
N
MSE
31
1_555
covale
1.347
A
MSE
9
A
C
MSE
31
1_555
A
PRO
10
A
N
PRO
32
1_555
covale
1.324
A
THR
61
A
C
THR
83
1_555
A
MSE
62
A
N
MSE
84
1_555
covale
1.337
A
MSE
62
A
C
MSE
84
1_555
A
ILE
63
A
N
ILE
85
1_555
covale
1.333
A
ASP
124
A
C
ASP
146
1_555
A
MSE
125
A
N
MSE
147
1_555
covale
1.322
A
MSE
125
A
C
MSE
147
1_555
A
ILE
126
A
N
ILE
148
1_555
covale
1.328
A
GLU
135
A
C
GLU
157
1_555
A
MSE
136
A
N
MSE
158
1_555
covale
1.329
A
MSE
136
A
C
MSE
158
1_555
A
GLY
137
A
N
GLY
159
1_555
covale
1.321
A
GLU
171
A
C
GLU
193
1_555
A
MSE
172
A
N
MSE
194
1_555
covale
1.342
A
MSE
172
A
C
MSE
194
1_555
A
GLU
173
A
N
GLU
195
1_555
covale
1.333
A
ASP
199
A
C
ASP
221
1_555
A
MSE
200
A
N
MSE
222
1_555
covale
1.328
A
MSE
200
A
C
MSE
222
1_555
A
ASP
201
A
N
ASP
223
1_555
covale
1.328
A
ILE
221
A
C
ILE
243
1_555
A
MSE
222
A
N
MSE
244
1_555
covale
1.331
A
MSE
222
A
C
MSE
244
1_555
A
LYS
223
A
N
LYS
245
1_555
covale
1.333
A
LYS
223
A
C
LYS
245
1_555
A
MSE
224
A
N
MSE
246
1_555
covale
1.328
A
MSE
224
A
C
MSE
246
1_555
A
VAL
225
A
N
VAL
247
1_555
HYDROLASE
Sulfurimonas denitrificans, 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase, adenine, Structural genomics, NYSGRC, New York Structural Genomics Research Consortium, PSI-Biology, HYDROLASE
Q30QR2_SULDN
UNP
1
2
Q30QR2
KIAIMGAMPEEISPILEKIGSYKSTSYAGNKYYEATYQGVELVIAYSKIGKVFSALSAATMIEHFGATKLLFSGVAGAIS
TNLKVGDLIVATKLSQHDLDITAFGHPYGYVPEGSVFVEADKDMIELSKKVALEMGKSVQEGIIATGDQFVANEERKNWI
GTTFGADALEMEGGSVGVVCNALNIPFFILRSISDAADMDASFSFDEFLESSAKESAEFIMKMVDELVALPLQDIK
2
237
4JWT
2
237
Q30QR2
A
1
24
259
1
EXPRESSION TAG
MSE
-21
4JWT
A
Q30QR2
UNP
1
1
EXPRESSION TAG
HIS
-20
4JWT
A
Q30QR2
UNP
2
1
EXPRESSION TAG
HIS
-19
4JWT
A
Q30QR2
UNP
3
1
EXPRESSION TAG
HIS
-18
4JWT
A
Q30QR2
UNP
4
1
EXPRESSION TAG
HIS
-17
4JWT
A
Q30QR2
UNP
5
1
EXPRESSION TAG
HIS
-16
4JWT
A
Q30QR2
UNP
6
1
EXPRESSION TAG
HIS
-15
4JWT
A
Q30QR2
UNP
7
1
EXPRESSION TAG
SER
-14
4JWT
A
Q30QR2
UNP
8
1
EXPRESSION TAG
SER
-13
4JWT
A
Q30QR2
UNP
9
1
EXPRESSION TAG
GLY
-12
4JWT
A
Q30QR2
UNP
10
1
EXPRESSION TAG
VAL
-11
4JWT
A
Q30QR2
UNP
11
1
EXPRESSION TAG
ASP
-10
4JWT
A
Q30QR2
UNP
12
1
EXPRESSION TAG
LEU
-9
4JWT
A
Q30QR2
UNP
13
1
EXPRESSION TAG
GLY
-8
4JWT
A
Q30QR2
UNP
14
1
EXPRESSION TAG
THR
-7
4JWT
A
Q30QR2
UNP
15
1
EXPRESSION TAG
GLU
-6
4JWT
A
Q30QR2
UNP
16
1
EXPRESSION TAG
ASN
-5
4JWT
A
Q30QR2
UNP
17
1
EXPRESSION TAG
LEU
-4
4JWT
A
Q30QR2
UNP
18
1
EXPRESSION TAG
TYR
-3
4JWT
A
Q30QR2
UNP
19
1
EXPRESSION TAG
PHE
-2
4JWT
A
Q30QR2
UNP
20
1
EXPRESSION TAG
GLN
-1
4JWT
A
Q30QR2
UNP
21
1
EXPRESSION TAG
SER
0
4JWT
A
Q30QR2
UNP
22
1
EXPRESSION TAG
MSE
1
4JWT
A
Q30QR2
UNP
23
9
8
anti-parallel
anti-parallel
parallel
parallel
anti-parallel
parallel
parallel
anti-parallel
anti-parallel
anti-parallel
parallel
parallel
parallel
anti-parallel
anti-parallel
A
LYS
24
A
LYS
46
A
TYR
28
A
TYR
50
A
ASN
31
A
ASN
53
A
TYR
38
A
TYR
60
A
VAL
41
A
VAL
63
A
TYR
47
A
TYR
69
A
LYS
2
A
LYS
24
A
GLY
7
A
GLY
29
A
LYS
70
A
LYS
92
A
ALA
79
A
ALA
101
A
ALA
169
A
ALA
191
A
GLU
171
A
GLU
193
A
VAL
140
A
VAL
162
A
THR
147
A
THR
169
A
LEU
89
A
LEU
111
A
GLN
97
A
GLN
119
A
VAL
119
A
VAL
141
A
GLU
120
A
GLU
142
A
LYS
24
A
LYS
46
A
TYR
28
A
TYR
50
A
ASN
31
A
ASN
53
A
TYR
38
A
TYR
60
A
VAL
41
A
VAL
63
A
TYR
47
A
TYR
69
A
LYS
2
A
LYS
24
A
GLY
7
A
GLY
29
A
LYS
70
A
LYS
92
A
ALA
79
A
ALA
101
A
PHE
188
A
PHE
210
A
ASP
196
A
ASP
218
A
LEU
89
A
LEU
111
A
GLN
97
A
GLN
119
A
VAL
119
A
VAL
141
A
GLU
120
A
GLU
142
BINDING SITE FOR RESIDUE EDO A 301
Software
4
BINDING SITE FOR RESIDUE EDO A 302
Software
5
BINDING SITE FOR RESIDUE EDO A 303
Software
4
BINDING SITE FOR RESIDUE EDO A 304
Software
5
BINDING SITE FOR RESIDUE ADE A 305
Software
12
A
TYR
28
A
TYR
50
4
1_555
A
ALA
29
A
ALA
51
4
1_555
A
GLY
30
A
GLY
52
4
1_555
A
ASN
185
A
ASN
207
4
10_665
A
GLU
120
A
GLU
142
5
1_555
A
ALA
121
A
ALA
143
5
1_555
A
ASP
122
A
ASP
144
5
1_555
A
LYS
123
A
LYS
145
5
1_555
A
HOH
443
G
HOH
5
1_555
A
TYR
-3
A
TYR
19
4
1_555
A
PHE
105
A
PHE
127
4
5_555
A
HOH
407
G
HOH
4
9_655
A
HOH
511
G
HOH
4
1_555
A
ASN
182
A
ASN
204
5
1_555
A
ASN
185
A
ASN
207
5
1_555
A
HOH
487
G
HOH
5
1_555
A
HOH
514
G
HOH
5
1_555
A
HOH
515
G
HOH
5
1_555
A
VAL
76
A
VAL
98
12
1_555
A
ALA
77
A
ALA
99
12
1_555
A
GLY
78
A
GLY
100
12
1_555
A
GLN
150
A
GLN
172
12
1_555
A
PHE
151
A
PHE
173
12
1_555
A
VAL
152
A
VAL
174
12
1_555
A
LEU
170
A
LEU
192
12
1_555
A
GLU
171
A
GLU
193
12
1_555
A
MSE
172
A
MSE
194
12
1_555
A
SER
195
A
SER
217
12
1_555
A
ASP
196
A
ASP
218
12
1_555
A
ALA
198
A
ALA
220
12
1_555
179
P 65 2 2