0.011616
0.000000
0.000000
0.000000
0.012091
0.000000
0.000000
0.000000
0.022289
0.00000
0.00000
0.00000
Chiu, T.K.
Sohn, C.
Johnson, R.C.
Dickerson, R.E.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
86.087
82.708
44.865
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
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O7 P
347.221
y
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
DNA linking
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA 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 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
C4 H12 N O3 1
122.143
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
non-polymer
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
O
N
59
N
P
N
60
N
O
N
61
N
O
N
62
N
O
N
63
N
C
N
64
R
C
N
65
N
O
N
66
S
C
N
67
N
O
N
68
N
C
N
69
R
C
Y
70
N
N
Y
71
N
C
Y
72
N
N
Y
73
N
C
Y
74
N
C
N
75
N
N
Y
76
N
N
Y
77
N
C
Y
78
N
N
Y
79
N
C
N
80
N
H
N
81
N
H
N
82
N
H
N
83
N
H
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
O
N
95
N
P
N
96
N
O
N
97
N
O
N
98
N
O
N
99
N
C
N
100
R
C
N
101
N
O
N
102
S
C
N
103
N
O
N
104
N
C
N
105
R
C
N
106
N
N
N
107
N
C
N
108
N
O
N
109
N
N
N
110
N
C
N
111
N
N
N
112
N
C
N
113
N
C
N
114
N
H
N
115
N
H
N
116
N
H
N
117
N
H
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
H
N
128
N
O
N
129
N
P
N
130
N
O
N
131
N
O
N
132
N
O
N
133
N
C
N
134
R
C
N
135
N
O
N
136
S
C
N
137
N
O
N
138
N
C
N
139
R
C
Y
140
N
N
Y
141
N
C
Y
142
N
N
Y
143
N
C
N
144
N
C
N
145
N
O
N
146
N
N
N
147
N
C
N
148
N
N
N
149
N
N
Y
150
N
C
N
151
N
H
N
152
N
H
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
O
N
166
N
P
N
167
N
O
N
168
N
O
N
169
N
O
N
170
N
C
N
171
R
C
N
172
N
O
N
173
S
C
N
174
N
O
N
175
N
C
N
176
R
C
N
177
N
N
N
178
N
C
N
179
N
O
N
180
N
N
N
181
N
C
N
182
N
O
N
183
N
C
N
184
N
C
N
185
N
C
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
H
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
N
N
202
S
C
N
203
N
C
N
204
N
O
N
205
N
C
N
206
N
C
N
207
N
C
N
208
N
O
N
209
N
N
N
210
N
O
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
N
N
222
S
C
N
223
N
C
N
224
N
O
N
225
N
C
N
226
N
C
N
227
N
C
N
228
N
O
N
229
N
O
N
230
N
O
N
231
N
H
N
232
N
H
N
233
N
H
N
234
N
H
N
235
N
H
N
236
N
H
N
237
N
H
N
238
N
H
N
239
N
H
N
240
N
N
N
241
N
C
N
242
N
C
N
243
N
O
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
N
N
251
S
C
N
252
N
C
N
253
N
O
N
254
N
C
Y
255
N
C
Y
256
N
N
Y
257
N
C
Y
258
N
C
Y
259
N
N
N
260
N
O
N
261
N
H
N
262
N
H
N
263
N
H
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
O
N
272
N
H
N
273
N
H
N
274
N
N
N
275
S
C
N
276
N
C
N
277
N
O
N
278
S
C
N
279
N
C
N
280
N
C
N
281
N
C
N
282
N
O
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
H
N
289
N
H
N
290
N
H
N
291
N
H
N
292
N
H
N
293
N
H
N
294
N
H
N
295
N
H
N
296
N
N
N
297
S
C
N
298
N
C
N
299
N
O
N
300
N
C
N
301
N
C
N
302
N
C
N
303
N
C
N
304
N
O
N
305
N
H
N
306
N
H
N
307
N
H
N
308
N
H
N
309
N
H
N
310
N
H
N
311
N
H
N
312
N
H
N
313
N
H
N
314
N
H
N
315
N
H
N
316
N
H
N
317
N
H
N
318
N
N
N
319
S
C
N
320
N
C
N
321
N
O
N
322
N
C
N
323
N
C
N
324
N
C
N
325
N
C
N
326
N
N
N
327
N
O
N
328
N
H
N
329
N
H
N
330
N
H
N
331
N
H
N
332
N
H
N
333
N
H
N
334
N
H
N
335
N
H
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
H
N
343
N
N
N
344
S
C
N
345
N
C
N
346
N
O
N
347
N
C
N
348
N
C
N
349
N
S
N
350
N
C
N
351
N
O
N
352
N
H
N
353
N
H
N
354
N
H
N
355
N
H
N
356
N
H
N
357
N
H
N
358
N
H
N
359
N
H
N
360
N
H
N
361
N
H
N
362
N
H
N
363
N
N
N
364
S
C
N
365
N
C
N
366
N
O
N
367
N
C
Y
368
N
C
Y
369
N
C
Y
370
N
C
Y
371
N
C
Y
372
N
C
Y
373
N
C
N
374
N
O
N
375
N
H
N
376
N
H
N
377
N
H
N
378
N
H
N
379
N
H
N
380
N
H
N
381
N
H
N
382
N
H
N
383
N
H
N
384
N
H
N
385
N
H
N
386
N
N
N
387
S
C
N
388
N
C
N
389
N
O
N
390
N
C
N
391
N
C
N
392
N
C
N
393
N
O
N
394
N
H
N
395
N
H
N
396
N
H
N
397
N
H
N
398
N
H
N
399
N
H
N
400
N
H
N
401
N
H
N
402
N
H
N
403
N
N
N
404
S
C
N
405
N
C
N
406
N
O
N
407
N
C
N
408
N
O
N
409
N
O
N
410
N
H
N
411
N
H
N
412
N
H
N
413
N
H
N
414
N
H
N
415
N
H
N
416
N
H
N
417
N
N
N
418
S
C
N
419
N
C
N
420
N
O
N
421
R
C
N
422
N
O
N
423
N
C
N
424
N
O
N
425
N
H
N
426
N
H
N
427
N
H
N
428
N
H
N
429
N
H
N
430
N
H
N
431
N
H
N
432
N
H
N
433
N
H
N
434
N
C
N
435
N
C
N
436
N
C
N
437
N
C
N
438
N
N
N
439
N
O
N
440
N
O
N
441
N
O
N
442
N
H
N
443
N
H
N
444
N
H
N
445
N
H
N
446
N
H
N
447
N
H
N
448
N
H
N
449
N
H
N
450
N
H
N
451
N
H
N
452
N
H
N
453
N
H
N
454
N
N
N
455
S
C
N
456
N
C
N
457
N
O
N
458
N
C
Y
459
N
C
Y
460
N
C
Y
461
N
C
Y
462
N
C
Y
463
N
C
Y
464
N
C
N
465
N
O
N
466
N
O
N
467
N
H
N
468
N
H
N
469
N
H
N
470
N
H
N
471
N
H
N
472
N
H
N
473
N
H
N
474
N
H
N
475
N
H
N
476
N
H
N
477
N
H
N
478
N
N
N
479
S
C
N
480
N
C
N
481
N
O
N
482
N
C
N
483
N
C
N
484
N
C
N
485
N
O
N
486
N
H
N
487
N
H
N
488
N
H
N
489
N
H
N
490
N
H
N
491
N
H
N
492
N
H
N
493
N
H
N
494
N
H
N
495
N
H
N
496
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
doub
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
sing
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
sing
N
77
N
sing
Y
78
N
sing
Y
79
N
sing
Y
80
N
doub
N
81
N
sing
Y
82
N
sing
Y
83
N
sing
Y
84
N
doub
N
85
N
sing
Y
86
N
doub
N
87
N
sing
N
88
N
sing
Y
89
N
sing
Y
90
N
doub
N
91
N
sing
Y
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
sing
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
sing
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
doub
N
119
N
sing
N
120
N
doub
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
doub
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
doub
N
131
N
sing
N
132
N
sing
N
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
sing
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
Y
151
N
sing
Y
152
N
sing
Y
153
N
doub
N
154
N
sing
Y
155
N
sing
N
156
N
sing
Y
157
N
doub
N
158
N
doub
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
doub
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
doub
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
sing
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
doub
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
doub
N
197
N
sing
N
198
N
sing
N
199
N
doub
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
sing
N
210
N
doub
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
doub
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
sing
N
229
N
doub
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
doub
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
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
doub
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
doub
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
Y
261
N
sing
Y
262
N
doub
Y
263
N
doub
N
264
N
sing
Y
265
N
sing
N
266
N
sing
Y
267
N
sing
N
268
N
sing
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
doub
N
280
N
sing
N
281
N
sing
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
sing
N
298
N
sing
N
299
N
sing
N
300
N
doub
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
sing
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
sing
N
313
N
sing
N
314
N
sing
N
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
doub
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
sing
N
335
N
sing
N
336
N
sing
N
337
N
sing
N
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
doub
N
346
N
sing
N
347
N
sing
N
348
N
sing
N
349
N
sing
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
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
doub
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
Y
369
N
doub
Y
370
N
sing
Y
371
N
sing
N
372
N
sing
Y
373
N
doub
N
374
N
sing
Y
375
N
doub
N
376
N
sing
Y
377
N
sing
N
378
N
sing
N
379
N
sing
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
sing
N
384
N
sing
N
385
N
sing
N
386
N
sing
N
387
N
doub
N
388
N
sing
N
389
N
sing
N
390
N
sing
N
391
N
sing
N
392
N
sing
N
393
N
sing
N
394
N
sing
N
395
N
sing
N
396
N
sing
N
397
N
sing
N
398
N
sing
N
399
N
sing
N
400
N
sing
N
401
N
sing
N
402
N
sing
N
403
N
sing
N
404
N
doub
N
405
N
sing
N
406
N
sing
N
407
N
sing
N
408
N
sing
N
409
N
sing
N
410
N
sing
N
411
N
sing
N
412
N
sing
N
413
N
sing
N
414
N
sing
N
415
N
sing
N
416
N
sing
N
417
N
doub
N
418
N
sing
N
419
N
sing
N
420
N
sing
N
421
N
sing
N
422
N
sing
N
423
N
sing
N
424
N
sing
N
425
N
sing
N
426
N
sing
N
427
N
sing
N
428
N
sing
N
429
N
sing
N
430
N
sing
N
431
N
sing
N
432
N
sing
N
433
N
sing
N
434
N
sing
N
435
N
sing
N
436
N
sing
N
437
N
sing
N
438
N
sing
N
439
N
sing
N
440
N
sing
N
441
N
sing
N
442
N
sing
N
443
N
sing
N
444
N
sing
N
445
N
sing
N
446
N
sing
N
447
N
sing
N
448
N
sing
N
449
N
sing
N
450
N
sing
N
451
N
sing
N
452
N
doub
N
453
N
sing
N
454
N
sing
N
455
N
sing
N
456
N
sing
Y
457
N
doub
Y
458
N
sing
Y
459
N
sing
N
460
N
sing
Y
461
N
doub
N
462
N
sing
Y
463
N
doub
N
464
N
sing
Y
465
N
sing
N
466
N
sing
N
467
N
sing
N
468
N
sing
N
469
N
sing
N
470
N
sing
N
471
N
sing
N
472
N
sing
N
473
N
sing
N
474
N
sing
N
475
N
sing
N
476
N
doub
N
477
N
sing
N
478
N
sing
N
479
N
sing
N
480
N
sing
N
481
N
sing
N
482
N
sing
N
483
N
sing
N
484
N
sing
N
485
N
sing
N
486
N
sing
N
487
N
sing
UK
EMBO J.
EMJODG
0897
0261-4189
21
801
814
10.1093/emboj/21.4.801
11847127
Testing water-mediated DNA recognition by the Hin recombinase.
2002
Thesis
145
241
How Hin Recombinase, FIS and Cations Bind DNA. Chapter 4. Water-Mediated Sequence-Specific Recognition by Hin Recombinase
2001
US
Science
SCIEAS
0038
0036-8075
263
348
355
Hin Recombinase Bound to DNA: The Origin of Specificity in Major and Minor Groove Interactions
1994
10.2210/pdb1jkr/pdb
pdb_00001jkr
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
CCD
1997-08-01
MOLECULAR REPLACEMENT WITH 1IJW HAVING THE PROPER DNA SUBSTITUTIONS AS THE STARTING MODEL.
M
x-ray
1
0.908
1.0
A1
CHESS
0.908
SYNCHROTRON
CHESS BEAMLINE A1
4309.826
5'-D(*TP*GP*TP*TP*TP*TP*TP*GP*AP*CP*AP*AP*GP*A)-3'
1
syn
polymer
4247.805
5'-D(*AP*TP*CP*TP*TP*GP*TP*CP*AP*AP*AP*AP*AP*C)-3'
1
syn
polymer
6047.051
DNA-INVERTASE HIN
RESIDUES 139 TO 190
1
syn
polymer
122.143
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
1
syn
non-polymer
18.015
water
2
nat
water
Hin Recombinase
no
no
(DT)(DG)(DT)(DT)(DT)(DT)(DT)(DG)(DA)(DC)(DA)(DA)(DG)(DA)
TGTTTTTGACAAGA
A
polydeoxyribonucleotide
no
no
(DA)(DT)(DC)(DT)(DT)(DG)(DT)(DC)(DA)(DA)(DA)(DA)(DA)(DC)
ATCTTGTCAAAAAC
B
polydeoxyribonucleotide
no
no
GRPRAINKHEQEQISRLLEKGHPRQQLAIIFGIGVSTLYRYFPASSIKKRMN
GRPRAINKHEQEQISRLLEKGHPRQQLAIIFGIGVSTLYRYFPASSIKKRMN
C
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
1
2.76
53.78
VAPOR DIFFUSION, HANGING DROP
8.50
HANGING DROP VAPOR DIFFUSION AT 4C,
WITH INITIAL CONCENTRATION IN DROP OF 0.10 MM DNA,
0.06 MM HIN, 10 MM TRIS (PH 8.5), 10 MM CACL2,
23 MM NACL, 2.5% V/V PEG400, AND 1.56 MM NA CACODYLATE.
RESERVOIR SOLUTION CONTAINS 100 MM TRIS (PH 8.5),
100 MM CACL2, 100 MM NACL, AND 25% PEG400.
CONCENTRATION OF PEG400 IN RESERVOIR SOLUTION WAS
INCREASED IN 5% INCREMENTS TO 35%., pH 8.50, VAPOR DIFFUSION, HANGING DROP
DNA
1
HIN
1
TRIS
1
CaCl2
1
NaCl
1
PEG 400
1
sodium cacodylate
1
Tris
2
CaCl2
2
NaCl
2
PEG 400
2
-22.437
1
19
A
3
B
29
-2.976
A_DG3:DC29_B
1
7.227
0.372
-0.820
0.192
-4.581
1
20
A
4
B
28
-14.995
A_DT4:DA28_B
2
-9.404
0.951
-0.338
-0.224
-1.157
1
20
A
5
B
27
0.373
A_DT5:DA27_B
3
-27.297
-0.079
-0.485
-0.133
-2.067
1
20
A
6
B
26
-3.281
A_DT6:DA26_B
4
-32.019
-0.005
-0.979
0.036
-2.925
1
20
A
7
B
25
-6.631
A_DT7:DA25_B
5
-17.969
-1.231
-0.355
-0.275
2.269
1
20
A
8
B
24
-0.251
A_DT8:DA24_B
6
-14.495
-0.555
-0.150
0.171
4.565
1
19
A
9
B
23
1.432
A_DG9:DC23_B
7
-15.734
-0.016
-0.086
-0.212
6.632
1
20
A
10
B
22
-6.971
A_DA10:DT22_B
8
-20.759
0.172
0.173
0.009
2.848
1
19
A
11
B
21
-4.892
A_DC11:DG21_B
9
-26.083
-0.193
0.130
-0.238
2.121
1
20
A
12
B
20
-4.107
A_DA12:DT20_B
10
-17.181
0.431
-0.138
-0.261
17.358
1
20
A
13
B
19
4.084
A_DA13:DT19_B
11
-7.505
0.432
0.400
-0.033
4.677
1
19
A
14
B
18
-4.561
A_DG14:DC18_B
12
-12.558
0.195
-0.073
-0.132
2.936
35.417
A
A
3
4
16.090
B
B
29
28
3.022
9.655
-1.077
-0.268
AA_DG3DT4:DA28DC29_BB
1
-3.680
6.134
33.922
-1.764
1.266
3.082
26.481
A
A
4
5
4.663
B
B
28
27
3.102
2.129
0.362
-0.397
AA_DT4DT5:DA27DA28_BB
2
3.220
-7.054
26.203
-1.403
0.019
3.178
37.462
A
A
5
6
17.843
B
B
27
26
3.176
11.275
-0.311
0.640
AA_DT5DT6:DA26DA27_BB
3
3.788
-5.995
35.588
-0.480
0.980
3.182
34.414
A
A
6
7
-4.638
B
B
26
25
3.258
-2.741
0.729
0.496
AA_DT6DT7:DA25DA26_BB
4
-1.271
2.151
34.285
1.260
-1.427
3.149
37.578
A
A
7
8
-3.295
B
B
25
24
3.133
-2.121
-0.158
-0.325
AA_DT7DT8:DA24DA25_BB
5
-1.083
1.683
37.505
-0.238
0.109
3.600
39.405
A
A
8
9
4.042
B
B
24
23
3.453
2.719
0.811
1.372
AA_DT8DG9:DC23DA24_BB
6
4.098
-6.093
39.109
1.687
-0.679
3.438
36.924
A
A
9
10
14.506
B
B
23
22
3.352
9.074
-1.002
0.348
AA_DG9DA10:DT22DC23_BB
7
-4.866
7.780
35.508
-0.749
0.885
3.415
33.044
A
A
10
11
1.625
B
B
22
21
3.448
0.924
0.570
-0.683
AA_DA10DC11:DG21DT22_BB
8
-0.712
1.251
33.024
-1.365
-1.129
3.553
39.070
A
A
11
12
3.563
B
B
21
20
3.522
2.381
-0.114
0.651
AA_DC11DA12:DT20DG21_BB
9
0.368
-0.550
38.998
0.664
0.218
2.647
29.262
A
A
12
13
-0.674
B
B
20
19
2.764
-0.340
0.705
-0.173
AA_DA12DA13:DT19DT20_BB
10
-3.970
7.883
28.996
-0.281
-2.109
3.482
35.695
A
A
13
14
9.296
B
B
19
18
3.647
5.675
-0.550
-0.661
AA_DA13DG14:DC18DT19_BB
11
1.159
-1.898
35.237
-1.979
1.080
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Refinement description
1
0
2002-02-22
1
1
2008-04-27
1
2
2011-07-13
1
3
2023-08-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Native wild-type Hin recombinase DNA-binding domain bound to underivatized
hixL half-site.
FORM1 BR18 DERIVATIVE
FORM1 I5 DERIVATIVE
FORM2 I4 DERIVATIVE
FORM1 A10G MUTANT
FORM1 T11G MUTANT
FORM1 G9T MUTANT
RCSB
Y
RCSB
2001-07-13
REL
REL
TRS
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
HOH
water
SYNTHETIC PEPTIDE
sample
1IJW
PDB
experimental model
TRS
204
4
TRS
TRS
204
A
HOH
202
5
HOH
HOH
202
B
HOH
203
5
HOH
HOH
203
C
T
2
n
1
DT
2
A
G
3
n
2
DG
3
A
T
4
n
3
DT
4
A
T
5
n
4
DT
5
A
T
6
n
5
DT
6
A
T
7
n
6
DT
7
A
T
8
n
7
DT
8
A
G
9
n
8
DG
9
A
A
10
n
9
DA
10
A
C
11
n
10
DC
11
A
A
12
n
11
DA
12
A
A
13
n
12
DA
13
A
G
14
n
13
DG
14
A
A
15
n
14
DA
15
A
A
16
n
1
DA
16
B
T
17
n
2
DT
17
B
C
18
n
3
DC
18
B
T
19
n
4
DT
19
B
T
20
n
5
DT
20
B
G
21
n
6
DG
21
B
T
22
n
7
DT
22
B
C
23
n
8
DC
23
B
A
24
n
9
DA
24
B
A
25
n
10
DA
25
B
A
26
n
11
DA
26
B
A
27
n
12
DA
27
B
A
28
n
13
DA
28
B
C
29
n
14
DC
29
B
GLY
139
n
1
GLY
139
C
ARG
140
n
2
ARG
140
C
PRO
141
n
3
PRO
141
C
ARG
142
n
4
ARG
142
C
ALA
143
n
5
ALA
143
C
ILE
144
n
6
ILE
144
C
ASN
145
n
7
ASN
145
C
LYS
146
n
8
LYS
146
C
HIS
147
n
9
HIS
147
C
GLU
148
n
10
GLU
148
C
GLN
149
n
11
GLN
149
C
GLU
150
n
12
GLU
150
C
GLN
151
n
13
GLN
151
C
ILE
152
n
14
ILE
152
C
SER
153
n
15
SER
153
C
ARG
154
n
16
ARG
154
C
LEU
155
n
17
LEU
155
C
LEU
156
n
18
LEU
156
C
GLU
157
n
19
GLU
157
C
LYS
158
n
20
LYS
158
C
GLY
159
n
21
GLY
159
C
HIS
160
n
22
HIS
160
C
PRO
161
n
23
PRO
161
C
ARG
162
n
24
ARG
162
C
GLN
163
n
25
GLN
163
C
GLN
164
n
26
GLN
164
C
LEU
165
n
27
LEU
165
C
ALA
166
n
28
ALA
166
C
ILE
167
n
29
ILE
167
C
ILE
168
n
30
ILE
168
C
PHE
169
n
31
PHE
169
C
GLY
170
n
32
GLY
170
C
ILE
171
n
33
ILE
171
C
GLY
172
n
34
GLY
172
C
VAL
173
n
35
VAL
173
C
SER
174
n
36
SER
174
C
THR
175
n
37
THR
175
C
LEU
176
n
38
LEU
176
C
TYR
177
n
39
TYR
177
C
ARG
178
n
40
ARG
178
C
TYR
179
n
41
TYR
179
C
PHE
180
n
42
PHE
180
C
PRO
181
n
43
PRO
181
C
ALA
182
n
44
ALA
182
C
SER
183
n
45
SER
183
C
SER
184
n
46
SER
184
C
n
47
185
C
n
48
186
C
n
49
187
C
n
50
188
C
n
51
189
C
n
52
190
C
author_defined_assembly
3
trimeric
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
C
CE
LYS
146
C
CE
LYS
8
1
Y
1
C
NZ
LYS
146
C
NZ
LYS
8
1
Y
1
C
CG
HIS
147
C
CG
HIS
9
1
Y
1
C
ND1
HIS
147
C
ND1
HIS
9
1
Y
1
C
CD2
HIS
147
C
CD2
HIS
9
1
Y
1
C
CE1
HIS
147
C
CE1
HIS
9
1
Y
1
C
NE2
HIS
147
C
NE2
HIS
9
1
Y
1
C
CG
GLU
150
C
CG
GLU
12
1
Y
1
C
CD
GLU
150
C
CD
GLU
12
1
Y
1
C
OE1
GLU
150
C
OE1
GLU
12
1
Y
1
C
OE2
GLU
150
C
OE2
GLU
12
1
Y
1
C
CG
GLU
157
C
CG
GLU
19
1
Y
1
C
CD
GLU
157
C
CD
GLU
19
1
Y
1
C
OE1
GLU
157
C
OE1
GLU
19
1
Y
1
C
OE2
GLU
157
C
OE2
GLU
19
1
Y
1
C
CG
LYS
158
C
CG
LYS
20
1
Y
1
C
CD
LYS
158
C
CD
LYS
20
1
Y
1
C
CE
LYS
158
C
CE
LYS
20
1
Y
1
C
NZ
LYS
158
C
NZ
LYS
20
1
Y
1
C
ILE
185
C
ILE
47
1
Y
1
C
LYS
186
C
LYS
48
1
Y
1
C
LYS
187
C
LYS
49
1
Y
1
C
ARG
188
C
ARG
50
1
Y
1
C
MET
189
C
MET
51
1
Y
1
C
ASN
190
C
ASN
52
1
Y
1
A
DT
7
0.094
SIDE CHAIN
1
A
DC
11
0.079
SIDE CHAIN
1
A
DA
15
0.088
SIDE CHAIN
1
B
DT
20
0.067
SIDE CHAIN
1
B
DA
28
0.095
SIDE CHAIN
1
C
TYR
179
0.069
SIDE CHAIN
1
8.59
1.20
110.70
119.29
A
A
A
O5'
P
OP2
DT
DT
DT
8
8
8
N
1
10.79
1.20
115.70
126.49
B
B
B
C5'
C4'
C3'
DA
DA
DA
16
16
16
A
N
1
7.64
1.20
115.70
123.34
B
B
B
C5'
C4'
C3'
DT
DT
DT
17
17
17
A
A
N
1
2.95
0.30
108.30
111.25
B
B
B
O4'
C1'
N9
DA
DA
DA
28
28
28
N
1
C
ASN
145
-65.63
-135.49
PROTEIN_REP.PARAM
PROTEIN.TOP
DNA-RNA_REP.PARAM
DNA-RNA.TOP
WATER_REP.PARAM
WATER.TOP
ION.PARAM
ION.TOP
60.20
15.107
0.00000
0.00000
2.251
0.00000
-17.359
0.3245000
0.2687000
0.2687000
2.28
24.80
707
7102
9.28
93.23
RANDOM
1
ANISOTROPIC_FIXED_ISOTROPIC
0.000
MOLECULAR REPLACEMENT
1IJW
MLF
100.00
0.25
0.55
0.47
5.00
0.66
0.80
2.28
24.80
2
939
8
576
353
0.013
1.720
19.440
1.882
8.51
4.000
11.44
6.000
11.62
6.000
15.66
7.000
0.4437000
0.4536000
2.38
66
610
8
7.04
72.14
69.00
2.28
24.8
1JKR
7102
0.000
0.8900000
1
15.68
17.0
93.23
2.28
2.38
2.49
0.2520000
2.60
72.14
refinement
CNS
data reduction
DENZO
data scaling
SCALEPACK
phasing
CNS
Testing the Water-Mediated HIN Recombinase DNA Recognition by Systematic Mutations
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
5
N
N
C
LYS
146
C
LYS
8
HELX_P
C
LYS
158
C
LYS
20
1
1
13
C
PRO
161
C
PRO
23
HELX_P
C
PHE
169
C
PHE
31
1
2
9
C
GLY
172
C
GLY
34
HELX_P
C
PHE
180
C
PHE
42
1
3
9
hydrog
WATSON-CRICK
A
DG
3
A
N1
DG
2
1_555
B
DC
29
B
N3
DC
14
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N2
DG
2
1_555
B
DC
29
B
O2
DC
14
1_555
hydrog
WATSON-CRICK
A
DG
3
A
O6
DG
2
1_555
B
DC
29
B
N4
DC
14
1_555
hydrog
WATSON-CRICK
A
DT
4
A
N3
DT
3
1_555
B
DA
28
B
N1
DA
13
1_555
hydrog
WATSON-CRICK
A
DT
4
A
O4
DT
3
1_555
B
DA
28
B
N6
DA
13
1_555
hydrog
WATSON-CRICK
A
DT
5
A
N3
DT
4
1_555
B
DA
27
B
N1
DA
12
1_555
hydrog
WATSON-CRICK
A
DT
5
A
O4
DT
4
1_555
B
DA
27
B
N6
DA
12
1_555
hydrog
WATSON-CRICK
A
DT
6
A
N3
DT
5
1_555
B
DA
26
B
N1
DA
11
1_555
hydrog
WATSON-CRICK
A
DT
6
A
O4
DT
5
1_555
B
DA
26
B
N6
DA
11
1_555
hydrog
WATSON-CRICK
A
DT
7
A
N3
DT
6
1_555
B
DA
25
B
N1
DA
10
1_555
hydrog
WATSON-CRICK
A
DT
7
A
O4
DT
6
1_555
B
DA
25
B
N6
DA
10
1_555
hydrog
WATSON-CRICK
A
DT
8
A
N3
DT
7
1_555
B
DA
24
B
N1
DA
9
1_555
hydrog
WATSON-CRICK
A
DT
8
A
O4
DT
7
1_555
B
DA
24
B
N6
DA
9
1_555
hydrog
WATSON-CRICK
A
DG
9
A
N1
DG
8
1_555
B
DC
23
B
N3
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
9
A
N2
DG
8
1_555
B
DC
23
B
O2
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
9
A
O6
DG
8
1_555
B
DC
23
B
N4
DC
8
1_555
hydrog
WATSON-CRICK
A
DA
10
A
N1
DA
9
1_555
B
DT
22
B
N3
DT
7
1_555
hydrog
WATSON-CRICK
A
DA
10
A
N6
DA
9
1_555
B
DT
22
B
O4
DT
7
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N3
DC
10
1_555
B
DG
21
B
N1
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N4
DC
10
1_555
B
DG
21
B
O6
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
11
A
O2
DC
10
1_555
B
DG
21
B
N2
DG
6
1_555
hydrog
WATSON-CRICK
A
DA
12
A
N1
DA
11
1_555
B
DT
20
B
N3
DT
5
1_555
hydrog
WATSON-CRICK
A
DA
12
A
N6
DA
11
1_555
B
DT
20
B
O4
DT
5
1_555
hydrog
WATSON-CRICK
A
DA
13
A
N1
DA
12
1_555
B
DT
19
B
N3
DT
4
1_555
hydrog
WATSON-CRICK
A
DA
13
A
N6
DA
12
1_555
B
DT
19
B
O4
DT
4
1_555
hydrog
WATSON-CRICK
A
DG
14
A
N1
DG
13
1_555
B
DC
18
B
N3
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
14
A
N2
DG
13
1_555
B
DC
18
B
O2
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
14
A
O6
DG
13
1_555
B
DC
18
B
N4
DC
3
1_555
DNA BINDING PROTEIN/DNA
WATER-MEDIATED RECOGNITION, PROTEIN-DNA COMPLEX, HIN RECOMBINASE, T11C MUTANT, DNA BINDING PROTEIN-DNA COMPLEX
HIN_SALTY
UNP
3
139
P03013
GRPRAINKHEQEQISRLLEKGHPRQQLAIIFGIGVSTLYRYFPASSIKKRMN
1JKR
PDB
1
1JKR
1JKR
PDB
2
1JKR
139
190
1JKR
139
190
P03013
C
1
1
52
2
15
1JKR
2
15
1JKR
A
2
1
14
16
29
1JKR
16
29
1JKR
B
3
1
14
BINDING SITE FOR RESIDUE TRS A 204
A
TRS
204
Software
4
A
DG
9
A
DG
8
4
1_555
A
DA
10
A
DA
9
4
1_555
B
DT
22
B
DT
7
4
6_554
B
DA
25
B
DA
10
4
1_555
20
C 2 2 21