1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Aramini, J.M.
Belote, R.L.
Ciccosanti, C.T.
Jiang, M.
Rost, B.
Nair, R.
Swapna, G.V.T.
Acton, T.B.
Xiao, R.
Everett, J.K.
Montelione, G.T.
Northeast Structural Genomics Consortium (NESG)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
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
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
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
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
N
1
N
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
O
N
7
N
H
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
N
N
15
S
C
N
16
N
C
N
17
N
O
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
N
N
22
N
C
N
23
N
N
N
24
N
N
N
25
N
O
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
H
N
39
N
H
N
40
N
H
N
41
N
N
N
42
S
C
N
43
N
C
N
44
N
O
N
45
N
C
N
46
N
C
N
47
N
O
N
48
N
N
N
49
N
O
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
N
N
59
S
C
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
N
64
N
O
N
65
N
O
N
66
N
O
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
N
N
75
S
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
C
N
80
N
C
N
81
N
O
N
82
N
N
N
83
N
O
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
N
N
95
S
C
N
96
N
C
N
97
N
O
N
98
N
C
N
99
N
C
N
100
N
C
N
101
N
O
N
102
N
O
N
103
N
O
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
H
N
110
N
H
N
111
N
H
N
112
N
H
N
113
N
N
N
114
N
C
N
115
N
C
N
116
N
O
N
117
N
O
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
N
N
124
S
C
N
125
N
C
N
126
N
O
N
127
N
C
Y
128
N
C
Y
129
N
N
Y
130
N
C
Y
131
N
C
Y
132
N
N
N
133
N
O
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
N
N
145
S
C
N
146
N
C
N
147
N
O
N
148
S
C
N
149
N
C
N
150
N
C
N
151
N
C
N
152
N
O
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
N
N
167
S
C
N
168
N
C
N
169
N
O
N
170
N
C
N
171
N
C
N
172
N
C
N
173
N
C
N
174
N
O
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
N
N
189
S
C
N
190
N
C
N
191
N
O
N
192
N
C
N
193
N
C
N
194
N
C
N
195
N
C
N
196
N
N
N
197
N
O
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
H
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
H
N
211
N
H
N
212
N
H
N
213
N
N
N
214
S
C
N
215
N
C
N
216
N
O
N
217
N
C
N
218
N
C
N
219
N
S
N
220
N
C
N
221
N
O
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
H
N
231
N
H
N
232
N
H
N
233
N
N
N
234
S
C
N
235
N
C
N
236
N
O
N
237
N
C
Y
238
N
C
Y
239
N
C
Y
240
N
C
Y
241
N
C
Y
242
N
C
Y
243
N
C
N
244
N
O
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
H
N
249
N
H
N
250
N
H
N
251
N
H
N
252
N
H
N
253
N
H
N
254
N
H
N
255
N
H
N
256
N
N
N
257
S
C
N
258
N
C
N
259
N
O
N
260
N
C
N
261
N
C
N
262
N
C
N
263
N
O
N
264
N
H
N
265
N
H
N
266
N
H
N
267
N
H
N
268
N
H
N
269
N
H
N
270
N
H
N
271
N
H
N
272
N
H
N
273
N
N
N
274
S
C
N
275
N
C
N
276
N
O
N
277
N
C
N
278
N
O
N
279
N
O
N
280
N
H
N
281
N
H
N
282
N
H
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
N
N
288
S
C
N
289
N
C
N
290
N
O
N
291
R
C
N
292
N
O
N
293
N
C
N
294
N
O
N
295
N
H
N
296
N
H
N
297
N
H
N
298
N
H
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
N
N
305
S
C
N
306
N
C
N
307
N
O
N
308
N
C
Y
309
N
C
Y
310
N
C
Y
311
N
C
Y
312
N
N
Y
313
N
C
Y
314
N
C
Y
315
N
C
Y
316
N
C
Y
317
N
C
N
318
N
O
N
319
N
H
N
320
N
H
N
321
N
H
N
322
N
H
N
323
N
H
N
324
N
H
N
325
N
H
N
326
N
H
N
327
N
H
N
328
N
H
N
329
N
H
N
330
N
H
N
331
N
N
N
332
S
C
N
333
N
C
N
334
N
O
N
335
N
C
Y
336
N
C
Y
337
N
C
Y
338
N
C
Y
339
N
C
Y
340
N
C
Y
341
N
C
N
342
N
O
N
343
N
O
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
H
N
352
N
H
N
353
N
H
N
354
N
H
N
355
N
N
N
356
S
C
N
357
N
C
N
358
N
O
N
359
N
C
N
360
N
C
N
361
N
C
N
362
N
O
N
363
N
H
N
364
N
H
N
365
N
H
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
H
N
373
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
doub
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
doub
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
doub
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
doub
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
doub
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
doub
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
doub
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
doub
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
doub
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
doub
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
Y
127
N
sing
Y
128
N
doub
Y
129
N
doub
N
130
N
sing
Y
131
N
sing
N
132
N
sing
Y
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
doub
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
doub
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
doub
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
doub
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
doub
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
Y
233
N
doub
Y
234
N
sing
Y
235
N
sing
N
236
N
sing
Y
237
N
doub
N
238
N
sing
Y
239
N
doub
N
240
N
sing
Y
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
doub
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
doub
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
doub
N
282
N
sing
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
doub
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
Y
302
N
doub
Y
303
N
sing
Y
304
N
sing
N
305
N
sing
Y
306
N
doub
Y
307
N
sing
Y
308
N
sing
N
309
N
sing
Y
310
N
sing
Y
311
N
doub
N
312
N
sing
Y
313
N
doub
N
314
N
sing
Y
315
N
sing
N
316
N
sing
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
doub
N
326
N
sing
N
327
N
sing
N
328
N
sing
N
329
N
sing
Y
330
N
doub
Y
331
N
sing
Y
332
N
sing
N
333
N
sing
Y
334
N
doub
N
335
N
sing
Y
336
N
doub
N
337
N
sing
Y
338
N
sing
N
339
N
sing
N
340
N
sing
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
N
345
N
sing
N
346
N
sing
N
347
N
sing
N
348
N
sing
N
349
N
doub
N
350
N
sing
N
351
N
sing
N
352
N
sing
N
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
sing
N
358
N
sing
N
359
N
sing
N
360
N
sing
To be Published
0353
Solution NMR structure of an O6-methylguanine DNA methyltransferase family protein from Vibrio parahaemolyticus. Northeast Structural Genomics Consortium target VpR247.
10.2210/pdb2kim/pdb
pdb_00002kim
12341.314
O6-methylguanine-DNA methyltransferase
1
man
polymer
Methylated-DNA-protein-cysteine methyltransferase-related protein
no
no
MDQFLVQIFAVIHQIPKGKVSTYGEIAKMAGYPGYARHVGKALGNLPEGSKLPWFRVINSQGKISLKGRDLDRQKQKLEA
EGIEVSEIGKIALRKYKWQPLEHHHHHH
MDQFLVQIFAVIHQIPKGKVSTYGEIAKMAGYPGYARHVGKALGNLPEGSKLPWFRVINSQGKISLKGRDLDRQKQKLEA
EGIEVSEIGKIALRKYKWQPLEHHHHHH
A
VpR247
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
sample
A79_1377, VP0951
419109
Vibrio parahaemolyticus AQ3810
469008
Escherichia coli BL21(DE3)
BL21(DE3)MGK
plasmid
VpR247-21.9
Structure solved using data obtained exclusively from a 1.7-mm microcyoprobe
Northeast Structural Genomics Consortium
NESG
PSI, Protein Structure Initiative
audit_author
pdbx_struct_assembly
pdbx_struct_oper_list
chem_comp_atom
chem_comp_bond
database_2
pdbx_nmr_software
pdbx_nmr_spectrometer
repository
Initial release
Version format compliance
Derived calculations
Structure summary
Data collection
Database references
1
0
2009-07-07
1
1
2011-07-13
1
2
2018-01-31
1
3
2024-05-01
_audit_author.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_pdbx_nmr_spectrometer.model
Y
BMRB
Y
RCSB
2009-05-07
REL
REL
1835
541
540
315
439
56
3
5
54
55
THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY, STATIC LIGHT SCATTERING AND 15N T1/T2 RELAXATION. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. SPECTRA FOR BACKBONE AND SIDE CHAIN ASSIGNMENTS AND NOESY SPECTRA USED FOR STRUCTURE CALCULATION WERE OBTAINED ON A 1.7-MM MICROCRYOPROBE AT 600 MHZ. BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN AND PINE, AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS WERE DETERMINED USING CYANA 3.0. BACKBONE (PHI/PSI) DIHEDRAL ANGLE CONSTRAINTS WERE OBTAINED FROM TALOS. HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING BOTH AUTOSTRUCTURE AND CYANA, AND WERE APPLIED ONLY IN THE FINAL REFINEMENT STAGE (CNS) OF THE STRUCTURE DETERMINATION. ROTAMER STATES OF SPECIFIC ORDERED RESIDUES WERE CONSTRAINED IN THE FINAL STAGE OF THE STRUCTURE REFINEMENT BASED ON PROCHECK AND MOLPROBITY. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HHHHHH): BACKBONE, 97.6%, SIDE CHAIN, 98.3%, AROMATICS, 100%, STEREOSPECIFIC METHYL, 100%, STEREOSPECIFIC SIDE CHAIN NH2: 100%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 TO 102, PSVS 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 3-32,35-47,51-67,69-100: (A) RMSD (ORDERED RESIDUES): BB, 0.6, HEAVY ATOM, 1.0. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 90.6%, ADDITIONALLY ALLOWED, 9.2%, GENEROUSLY ALLOWED, 0.0%, DISALLOWED, 0.1%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.13/-0.20, ALL, -0.04/-0.24. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 20.04/-1.91 (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 1-102): RECALL, 0.982, PRECISION, 0.910, F-MEASURE, 0.945, DP-SCORE, 0.788. (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 16. (G) MOLPROBITY RAMACHANDRAN ANALYSIS (ALL RESIDUES): THE C-TERMINAL HIS TAG RESIDUES OF THE PROTEIN (HHHHHH) WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS AND HAVE BEEN OMITTED FROM THIS DEPOSITION. COORDINATES FOR THE FOLLOWING RESIDUES ARE NOT WELL DETERMINED [S(PHI) + S(PSI) < 1.8]: 1-2,33-34,48-50,68,101-102.
structures with the lowest energy
100
20
4.9
0.29
0.01
2D 1H-15N HSQC
2D 1H-13C HSQC
3D 1H-13C NOESY aliphatic
3D 1H-13C NOESY aromatic
3D HNCO
3D HN(CA)CO
3D HNCA
3D CBCA(CO)NH
3D HNCACB
3D HBHA(CO)NH
3D HCCH-COSY aliphatic
3D HCCH-TOCSY aliphatic
3D (H)CCH-TOCSY aliphatic
3D HNHA
3D HN(CO)CA
2D 1H-15N hetNOE
1D 1H-15N T1 and T2
2D 1H-13C HSQC high res. (L/V methyl stereoassignment)
3D 1H-15N NOESY
0.94
mM
[U-100% 13C; U-100% 15N]
20
mM
200
mM
5
mM
10
mM
0.02
%
50
uM
0.92
mM
[U-5% 13C; U-100% 15N]
20
mM
200
mM
5
mM
10
mM
0.02
%
50
uM
0.2
6.5
ambient
298
K
THE FINAL STRUCTURES ARE BASED ON A TOTAL OF 1835 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 117 DIHEDRAL ANGLE CONSTRAINTS, AND 56 HYDROGEN BOND CONSTRAINTS (19.9 CONSTRAINTS PER RESIDUE, 5.4 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 102 BY PSVS 1.3). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA 3.0. THE 20 STRUCTURES OUT OF 100 WITH THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) WITH PARAM19, AND USING NEUTRAL HISTIDINES (NE2H TAUTOMER) AT POSITIONS 13 and 38.
simulated annealing
1
lowest energy
0.94 mM [U-100% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 90% H2O/10% D2O
90% H2O/10% D2O
0.92 mM [U-5% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 90% H2O/10% D2O
90% H2O/10% D2O
Bruker Biospin
collection
TopSpin
2.1
Bruker Biospin
data analysis
TopSpin
2.1
Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
processing
NMRPipe
2.3
Goddard
data analysis
Sparky
3.112
Goddard
peak picking
Sparky
3.112
Bahrami, Markley, Assadi, and Eghbalnia
chemical shift assignment
PINE
1.0
Zimmerman, Moseley, Kulikowski and Montelione
chemical shift assignment
AutoAssign
2.4.0
Zimmerman, Moseley, Kulikowski and Montelione
validation
AutoAssign
2.4.0
Guntert, Mumenthaler and Wuthrich
structure solution
CYANA
3.0
Brunger, Adams, Clore, Gros, Nilges and Read
refinement
CNS
1.2
Huang, Tejero, Powers and Montelione
rpf analysis
AutoStructure
2.2.1
Bhattacharya and Montelione
structure quality analysis
PSVS
1.3
Richardson
structure quality analysis
MolProbity
3.15
Tejero and Montelione
pdb coordinate analysis
PdbStat
5.1
600
Bruker
AVANCE
Bruker Avance
MET
1
n
1
MET
1
A
ASP
2
n
2
ASP
2
A
GLN
3
n
3
GLN
3
A
PHE
4
n
4
PHE
4
A
LEU
5
n
5
LEU
5
A
VAL
6
n
6
VAL
6
A
GLN
7
n
7
GLN
7
A
ILE
8
n
8
ILE
8
A
PHE
9
n
9
PHE
9
A
ALA
10
n
10
ALA
10
A
VAL
11
n
11
VAL
11
A
ILE
12
n
12
ILE
12
A
HIS
13
n
13
HIS
13
A
GLN
14
n
14
GLN
14
A
ILE
15
n
15
ILE
15
A
PRO
16
n
16
PRO
16
A
LYS
17
n
17
LYS
17
A
GLY
18
n
18
GLY
18
A
LYS
19
n
19
LYS
19
A
VAL
20
n
20
VAL
20
A
SER
21
n
21
SER
21
A
THR
22
n
22
THR
22
A
TYR
23
n
23
TYR
23
A
GLY
24
n
24
GLY
24
A
GLU
25
n
25
GLU
25
A
ILE
26
n
26
ILE
26
A
ALA
27
n
27
ALA
27
A
LYS
28
n
28
LYS
28
A
MET
29
n
29
MET
29
A
ALA
30
n
30
ALA
30
A
GLY
31
n
31
GLY
31
A
TYR
32
n
32
TYR
32
A
PRO
33
n
33
PRO
33
A
GLY
34
n
34
GLY
34
A
TYR
35
n
35
TYR
35
A
ALA
36
n
36
ALA
36
A
ARG
37
n
37
ARG
37
A
HIS
38
n
38
HIS
38
A
VAL
39
n
39
VAL
39
A
GLY
40
n
40
GLY
40
A
LYS
41
n
41
LYS
41
A
ALA
42
n
42
ALA
42
A
LEU
43
n
43
LEU
43
A
GLY
44
n
44
GLY
44
A
ASN
45
n
45
ASN
45
A
LEU
46
n
46
LEU
46
A
PRO
47
n
47
PRO
47
A
GLU
48
n
48
GLU
48
A
GLY
49
n
49
GLY
49
A
SER
50
n
50
SER
50
A
LYS
51
n
51
LYS
51
A
LEU
52
n
52
LEU
52
A
PRO
53
n
53
PRO
53
A
TRP
54
n
54
TRP
54
A
PHE
55
n
55
PHE
55
A
ARG
56
n
56
ARG
56
A
VAL
57
n
57
VAL
57
A
ILE
58
n
58
ILE
58
A
ASN
59
n
59
ASN
59
A
SER
60
n
60
SER
60
A
GLN
61
n
61
GLN
61
A
GLY
62
n
62
GLY
62
A
LYS
63
n
63
LYS
63
A
ILE
64
n
64
ILE
64
A
SER
65
n
65
SER
65
A
LEU
66
n
66
LEU
66
A
LYS
67
n
67
LYS
67
A
GLY
68
n
68
GLY
68
A
ARG
69
n
69
ARG
69
A
ASP
70
n
70
ASP
70
A
LEU
71
n
71
LEU
71
A
ASP
72
n
72
ASP
72
A
ARG
73
n
73
ARG
73
A
GLN
74
n
74
GLN
74
A
LYS
75
n
75
LYS
75
A
GLN
76
n
76
GLN
76
A
LYS
77
n
77
LYS
77
A
LEU
78
n
78
LEU
78
A
GLU
79
n
79
GLU
79
A
ALA
80
n
80
ALA
80
A
GLU
81
n
81
GLU
81
A
GLY
82
n
82
GLY
82
A
ILE
83
n
83
ILE
83
A
GLU
84
n
84
GLU
84
A
VAL
85
n
85
VAL
85
A
SER
86
n
86
SER
86
A
GLU
87
n
87
GLU
87
A
ILE
88
n
88
ILE
88
A
GLY
89
n
89
GLY
89
A
LYS
90
n
90
LYS
90
A
ILE
91
n
91
ILE
91
A
ALA
92
n
92
ALA
92
A
LEU
93
n
93
LEU
93
A
ARG
94
n
94
ARG
94
A
LYS
95
n
95
LYS
95
A
TYR
96
n
96
TYR
96
A
LYS
97
n
97
LYS
97
A
TRP
98
n
98
TRP
98
A
GLN
99
n
99
GLN
99
A
PRO
100
n
100
PRO
100
A
LEU
101
n
101
LEU
101
A
GLU
102
n
102
GLU
102
A
n
103
103
A
n
104
104
A
n
105
105
A
n
106
106
A
n
107
107
A
n
108
108
A
author_defined_assembly
1
monomeric
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
identity operation
0.0000000000
0.0000000000
0.0000000000
A
N
SER
21
A
N
SER
21
A
O
ILE
58
A
O
ILE
58
1
A
HIS
103
A
HIS
103
1
Y
1
A
HIS
104
A
HIS
104
1
Y
1
A
HIS
105
A
HIS
105
1
Y
1
A
HIS
106
A
HIS
106
1
Y
1
A
HIS
107
A
HIS
107
1
Y
1
A
HIS
108
A
HIS
108
1
Y
2
A
HIS
103
A
HIS
103
1
Y
2
A
HIS
104
A
HIS
104
1
Y
2
A
HIS
105
A
HIS
105
1
Y
2
A
HIS
106
A
HIS
106
1
Y
2
A
HIS
107
A
HIS
107
1
Y
2
A
HIS
108
A
HIS
108
1
Y
3
A
HIS
103
A
HIS
103
1
Y
3
A
HIS
104
A
HIS
104
1
Y
3
A
HIS
105
A
HIS
105
1
Y
3
A
HIS
106
A
HIS
106
1
Y
3
A
HIS
107
A
HIS
107
1
Y
3
A
HIS
108
A
HIS
108
1
Y
4
A
HIS
103
A
HIS
103
1
Y
4
A
HIS
104
A
HIS
104
1
Y
4
A
HIS
105
A
HIS
105
1
Y
4
A
HIS
106
A
HIS
106
1
Y
4
A
HIS
107
A
HIS
107
1
Y
4
A
HIS
108
A
HIS
108
1
Y
5
A
HIS
103
A
HIS
103
1
Y
5
A
HIS
104
A
HIS
104
1
Y
5
A
HIS
105
A
HIS
105
1
Y
5
A
HIS
106
A
HIS
106
1
Y
5
A
HIS
107
A
HIS
107
1
Y
5
A
HIS
108
A
HIS
108
1
Y
6
A
HIS
103
A
HIS
103
1
Y
6
A
HIS
104
A
HIS
104
1
Y
6
A
HIS
105
A
HIS
105
1
Y
6
A
HIS
106
A
HIS
106
1
Y
6
A
HIS
107
A
HIS
107
1
Y
6
A
HIS
108
A
HIS
108
1
Y
7
A
HIS
103
A
HIS
103
1
Y
7
A
HIS
104
A
HIS
104
1
Y
7
A
HIS
105
A
HIS
105
1
Y
7
A
HIS
106
A
HIS
106
1
Y
7
A
HIS
107
A
HIS
107
1
Y
7
A
HIS
108
A
HIS
108
1
Y
8
A
HIS
103
A
HIS
103
1
Y
8
A
HIS
104
A
HIS
104
1
Y
8
A
HIS
105
A
HIS
105
1
Y
8
A
HIS
106
A
HIS
106
1
Y
8
A
HIS
107
A
HIS
107
1
Y
8
A
HIS
108
A
HIS
108
1
Y
9
A
HIS
103
A
HIS
103
1
Y
9
A
HIS
104
A
HIS
104
1
Y
9
A
HIS
105
A
HIS
105
1
Y
9
A
HIS
106
A
HIS
106
1
Y
9
A
HIS
107
A
HIS
107
1
Y
9
A
HIS
108
A
HIS
108
1
Y
10
A
HIS
103
A
HIS
103
1
Y
10
A
HIS
104
A
HIS
104
1
Y
10
A
HIS
105
A
HIS
105
1
Y
10
A
HIS
106
A
HIS
106
1
Y
10
A
HIS
107
A
HIS
107
1
Y
10
A
HIS
108
A
HIS
108
1
Y
11
A
HIS
103
A
HIS
103
1
Y
11
A
HIS
104
A
HIS
104
1
Y
11
A
HIS
105
A
HIS
105
1
Y
11
A
HIS
106
A
HIS
106
1
Y
11
A
HIS
107
A
HIS
107
1
Y
11
A
HIS
108
A
HIS
108
1
Y
12
A
HIS
103
A
HIS
103
1
Y
12
A
HIS
104
A
HIS
104
1
Y
12
A
HIS
105
A
HIS
105
1
Y
12
A
HIS
106
A
HIS
106
1
Y
12
A
HIS
107
A
HIS
107
1
Y
12
A
HIS
108
A
HIS
108
1
Y
13
A
HIS
103
A
HIS
103
1
Y
13
A
HIS
104
A
HIS
104
1
Y
13
A
HIS
105
A
HIS
105
1
Y
13
A
HIS
106
A
HIS
106
1
Y
13
A
HIS
107
A
HIS
107
1
Y
13
A
HIS
108
A
HIS
108
1
Y
14
A
HIS
103
A
HIS
103
1
Y
14
A
HIS
104
A
HIS
104
1
Y
14
A
HIS
105
A
HIS
105
1
Y
14
A
HIS
106
A
HIS
106
1
Y
14
A
HIS
107
A
HIS
107
1
Y
14
A
HIS
108
A
HIS
108
1
Y
15
A
HIS
103
A
HIS
103
1
Y
15
A
HIS
104
A
HIS
104
1
Y
15
A
HIS
105
A
HIS
105
1
Y
15
A
HIS
106
A
HIS
106
1
Y
15
A
HIS
107
A
HIS
107
1
Y
15
A
HIS
108
A
HIS
108
1
Y
16
A
HIS
103
A
HIS
103
1
Y
16
A
HIS
104
A
HIS
104
1
Y
16
A
HIS
105
A
HIS
105
1
Y
16
A
HIS
106
A
HIS
106
1
Y
16
A
HIS
107
A
HIS
107
1
Y
16
A
HIS
108
A
HIS
108
1
Y
17
A
HIS
103
A
HIS
103
1
Y
17
A
HIS
104
A
HIS
104
1
Y
17
A
HIS
105
A
HIS
105
1
Y
17
A
HIS
106
A
HIS
106
1
Y
17
A
HIS
107
A
HIS
107
1
Y
17
A
HIS
108
A
HIS
108
1
Y
18
A
HIS
103
A
HIS
103
1
Y
18
A
HIS
104
A
HIS
104
1
Y
18
A
HIS
105
A
HIS
105
1
Y
18
A
HIS
106
A
HIS
106
1
Y
18
A
HIS
107
A
HIS
107
1
Y
18
A
HIS
108
A
HIS
108
1
Y
19
A
HIS
103
A
HIS
103
1
Y
19
A
HIS
104
A
HIS
104
1
Y
19
A
HIS
105
A
HIS
105
1
Y
19
A
HIS
106
A
HIS
106
1
Y
19
A
HIS
107
A
HIS
107
1
Y
19
A
HIS
108
A
HIS
108
1
Y
20
A
HIS
103
A
HIS
103
1
Y
20
A
HIS
104
A
HIS
104
1
Y
20
A
HIS
105
A
HIS
105
1
Y
20
A
HIS
106
A
HIS
106
1
Y
20
A
HIS
107
A
HIS
107
1
Y
20
A
HIS
108
A
HIS
108
1
Y
11
A
A
HA
HH22
LYS
ARG
17
56
1.27
1
A
SER
60
-69.91
0.50
2
A
TYR
35
-91.85
30.13
2
A
GLU
84
-68.92
92.52
3
A
LYS
17
-69.44
89.61
3
A
ALA
92
-67.65
94.51
3
A
PRO
100
-72.66
35.21
4
A
LYS
17
-67.30
99.27
5
A
LYS
17
-62.54
95.69
5
A
TYR
35
-74.91
27.54
6
A
LYS
17
-60.91
95.39
6
A
PRO
53
-68.89
94.49
6
A
PHE
55
-67.32
1.00
6
A
LEU
101
-88.65
31.26
7
A
ILE
58
-118.38
-168.89
8
A
GLU
84
-67.64
92.03
9
A
GLU
84
-68.17
95.92
10
A
ASP
2
-173.99
128.07
10
A
TYR
35
-141.89
21.50
10
A
PRO
53
-66.01
95.36
10
A
ILE
58
-115.94
-169.31
10
A
GLU
84
-67.62
92.20
10
A
ALA
92
-63.63
94.65
11
A
GLN
3
68.80
-30.03
11
A
LEU
101
-131.47
-66.55
12
A
TYR
32
-140.28
58.09
12
A
PRO
53
-65.13
95.51
12
A
ALA
92
-69.02
92.83
13
A
ASN
45
-150.62
14.17
13
A
ILE
58
-123.27
-169.12
14
A
LYS
17
-63.73
85.88
14
A
TYR
35
-79.01
36.01
14
A
ILE
58
-109.82
-169.81
17
A
ILE
58
-125.18
-169.70
17
A
GLN
99
-150.97
87.70
18
A
LYS
19
-65.56
99.05
18
A
PRO
33
-76.45
30.99
18
A
PRO
47
-72.49
-165.92
18
A
LYS
51
74.57
-47.91
18
A
SER
65
-88.11
30.22
18
A
GLU
84
-67.17
91.95
19
A
TYR
35
-79.01
46.98
19
A
PHE
55
-69.62
1.88
19
A
SER
60
-65.18
4.48
20
A
TYR
35
-83.52
36.88
20
A
PRO
53
-68.23
94.61
20
A
ALA
92
-62.62
95.96
20
A
LEU
101
-160.19
23.20
lowest energy, model 1
1.7-mm microcryoprobe solution NMR structure of an O6-methylguanine DNA methyltransferase family protein from Vibrio parahaemolyticus. Northeast Structural Genomics Consortium target VpR247.
1
N
N
A
ASP
2
A
ASP
2
HELX_P
A
HIS
13
A
HIS
13
1
1
12
A
TYR
23
A
TYR
23
HELX_P
A
GLY
31
A
GLY
31
1
2
9
A
TYR
35
A
TYR
35
HELX_P
A
GLY
44
A
GLY
44
1
3
10
A
PRO
53
A
PRO
53
HELX_P
A
PHE
55
A
PHE
55
5
4
3
A
GLY
68
A
GLY
68
HELX_P
A
ALA
80
A
ALA
80
1
5
13
A
ALA
92
A
ALA
92
HELX_P
A
LYS
97
A
LYS
97
1
6
6
TRANSFERASE
Methods Development, solution NMR structure, DNA base repair, O6 methylguanine methyltransferase, NESG, PSI-2, Methyltransferase, Transferase, Structural Genomics, Protein Structure Initiative, Northeast Structural Genomics Consortium
A6B4U8_VIBPA
UNP
1
1
A6B4U8
MDQFLVQIFAVIHQIPKGKVSTYGEIAKMAGYPGYARHVGKALGNLPEGSKLPWFRVINSQGKISLKGRDLDRQKQKLEA
EGIEVSEIGKIALRKYKWQP
1
100
2KIM
1
100
A6B4U8
A
1
1
100
1
expression tag
LEU
101
2KIM
A
A6B4U8
UNP
101
1
expression tag
GLU
102
2KIM
A
A6B4U8
UNP
102
1
expression tag
HIS
103
2KIM
A
A6B4U8
UNP
103
1
expression tag
HIS
104
2KIM
A
A6B4U8
UNP
104
1
expression tag
HIS
105
2KIM
A
A6B4U8
UNP
105
1
expression tag
HIS
106
2KIM
A
A6B4U8
UNP
106
1
expression tag
HIS
107
2KIM
A
A6B4U8
UNP
107
1
expression tag
HIS
108
2KIM
A
A6B4U8
UNP
108
2
parallel
A
SER
21
A
SER
21
A
THR
22
A
THR
22
A
VAL
57
A
VAL
57
A
ILE
58
A
ILE
58