0.011743
0.000000
0.000000
0.000000
0.012098
0.000000
0.000000
0.000000
0.022161
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
85.158
82.656
45.124
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
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
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
N
N
272
S
C
N
273
N
C
N
274
N
O
N
275
S
C
N
276
N
C
N
277
N
C
N
278
N
C
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
H
N
288
N
H
N
289
N
H
N
290
N
H
N
291
N
H
N
292
N
H
N
293
N
N
N
294
S
C
N
295
N
C
N
296
N
O
N
297
N
C
N
298
N
C
N
299
N
C
N
300
N
C
N
301
N
O
N
302
N
H
N
303
N
H
N
304
N
H
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
N
N
316
S
C
N
317
N
C
N
318
N
O
N
319
N
C
N
320
N
C
N
321
N
C
N
322
N
C
N
323
N
N
N
324
N
O
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
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
N
N
341
S
C
N
342
N
C
N
343
N
O
N
344
N
C
N
345
N
C
N
346
N
S
N
347
N
C
N
348
N
O
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
H
N
356
N
H
N
357
N
H
N
358
N
H
N
359
N
H
N
360
N
N
N
361
S
C
N
362
N
C
N
363
N
O
N
364
N
C
Y
365
N
C
Y
366
N
C
Y
367
N
C
Y
368
N
C
Y
369
N
C
Y
370
N
C
N
371
N
O
N
372
N
H
N
373
N
H
N
374
N
H
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
N
N
384
S
C
N
385
N
C
N
386
N
O
N
387
N
C
N
388
N
C
N
389
N
C
N
390
N
O
N
391
N
H
N
392
N
H
N
393
N
H
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
N
N
401
S
C
N
402
N
C
N
403
N
O
N
404
N
C
N
405
N
O
N
406
N
O
N
407
N
H
N
408
N
H
N
409
N
H
N
410
N
H
N
411
N
H
N
412
N
H
N
413
N
H
N
414
N
N
N
415
S
C
N
416
N
C
N
417
N
O
N
418
R
C
N
419
N
O
N
420
N
C
N
421
N
O
N
422
N
H
N
423
N
H
N
424
N
H
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
N
N
432
S
C
N
433
N
C
N
434
N
O
N
435
N
C
Y
436
N
C
Y
437
N
C
Y
438
N
C
Y
439
N
C
Y
440
N
C
Y
441
N
C
N
442
N
O
N
443
N
O
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
H
N
455
N
N
N
456
S
C
N
457
N
C
N
458
N
O
N
459
N
C
N
460
N
C
N
461
N
C
N
462
N
O
N
463
N
H
N
464
N
H
N
465
N
H
N
466
N
H
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
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
doub
N
278
N
sing
N
279
N
sing
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
doub
N
299
N
sing
N
300
N
sing
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
doub
N
320
N
sing
N
321
N
sing
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
doub
N
344
N
sing
N
345
N
sing
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
doub
N
363
N
sing
N
364
N
sing
N
365
N
sing
N
366
N
sing
Y
367
N
doub
Y
368
N
sing
Y
369
N
sing
N
370
N
sing
Y
371
N
doub
N
372
N
sing
Y
373
N
doub
N
374
N
sing
Y
375
N
sing
N
376
N
sing
N
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
doub
N
386
N
sing
N
387
N
sing
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
doub
N
403
N
sing
N
404
N
sing
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
doub
N
416
N
sing
N
417
N
sing
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
doub
N
432
N
sing
N
433
N
sing
N
434
N
sing
N
435
N
sing
Y
436
N
doub
Y
437
N
sing
Y
438
N
sing
N
439
N
sing
Y
440
N
doub
N
441
N
sing
Y
442
N
doub
N
443
N
sing
Y
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
sing
N
453
N
sing
N
454
N
sing
N
455
N
doub
N
456
N
sing
N
457
N
sing
N
458
N
sing
N
459
N
sing
N
460
N
sing
N
461
N
sing
N
462
N
sing
N
463
N
sing
N
464
N
sing
N
465
N
sing
N
466
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/pdb1jkq/pdb
pdb_00001jkq
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
IMAGE PLATE
1997-09-01
MAR scanner 300 mm plate
MOLECULAR REPLACEMENT WITH 1IJW HAVING THE PROPER DNA SUBSTITUTIONS AS THE STARTING MODEL.
M
x-ray
1
1.100
1.0
X25
NSLS
1.100
SYNCHROTRON
NSLS BEAMLINE X25
4299.824
5'-D(*TP*GP*TP*TP*TP*TP*TP*TP*AP*TP*AP*AP*GP*A)-3'
1
syn
polymer
4255.831
5'-D(*AP*TP*CP*TP*TP*AP*TP*AP*AP*AP*AP*AP*AP*C)-3'
1
syn
polymer
6047.051
DNA-INVERTASE HIN
RESIDUES 139 TO 190
1
syn
polymer
Hin Recombinase
no
no
(DT)(DG)(DT)(DT)(DT)(DT)(DT)(DT)(DA)(DT)(DA)(DA)(DG)(DA)
TGTTTTTTATAAGA
A
polydeoxyribonucleotide
no
no
(DA)(DT)(DC)(DT)(DT)(DA)(DT)(DA)(DA)(DA)(DA)(DA)(DA)(DC)
ATCTTATAAAAAAC
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
2.74
53.36
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, 20 MM HEPES (PH 7.5), 20 MM CACL2,
33 MM NACL, 5.0% V/V PEG400, AND 1.56 MM NA CACODYLATE.
RESERVOIR SOLUTION CONTAINS 100 MM HEPES (PH 7.5), 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
HEPES
1
CaCl2
1
NaCl
1
PEG 400
1
sodium cacodylate
1
HEPES
2
CaCl2
2
NaCl
2
PEG 400
2
-16.587
1
19
A
3
B
29
-5.900
A_DG3:DC29_B
1
10.262
0.197
-0.685
-0.183
3.843
1
20
A
4
B
28
1.897
A_DT4:DA28_B
2
-9.287
-0.225
-0.136
-0.271
-2.395
1
20
A
5
B
27
-0.292
A_DT5:DA27_B
3
-15.104
-1.285
-0.100
-0.008
-2.456
1
20
A
6
B
26
-3.330
A_DT6:DA26_B
4
-20.791
0.204
-0.119
-0.257
-2.549
1
20
A
7
B
25
-6.358
A_DT7:DA25_B
5
0.872
-1.658
-0.415
-0.248
-5.122
1
20
A
8
B
24
4.583
A_DT8:DA24_B
6
-8.877
-1.209
-0.128
0.155
-1.754
1
20
A
9
B
23
-0.677
A_DT9:DA23_B
7
-6.321
-0.690
-0.151
-0.062
-1.143
1
20
A
10
B
22
-2.185
A_DA10:DT22_B
8
-9.786
-1.016
0.122
-0.695
-0.966
1
20
A
11
B
21
-11.561
A_DT11:DA21_B
9
-2.438
-0.988
0.007
-0.424
-5.155
1
20
A
12
B
20
-3.085
A_DA12:DT20_B
10
-10.106
0.394
-0.157
-0.296
10.089
1
20
A
13
B
19
1.768
A_DA13:DT19_B
11
-2.744
0.442
0.438
-0.335
5.082
1
19
A
14
B
18
-3.069
A_DG14:DC18_B
12
-3.653
0.231
0.271
-0.334
2.957
27.029
A
A
3
4
10.666
B
B
29
28
2.966
4.929
-0.456
0.034
AA_DG3DT4:DA28DC29_BB
1
-5.057
10.942
26.107
-1.082
-0.209
3.008
28.128
A
A
4
5
8.718
B
B
28
27
3.140
4.216
0.139
-0.670
AA_DT4DT5:DA27DA28_BB
2
2.506
-5.181
27.706
-2.314
0.271
3.306
46.120
A
A
5
6
4.221
B
B
27
26
3.289
3.300
-0.007
0.527
AA_DT5DT6:DA26DA27_BB
3
3.944
-5.044
45.848
0.387
0.350
3.259
27.358
A
A
6
7
-2.420
B
B
26
25
3.199
-1.141
0.648
-0.087
AA_DT6DT7:DA25DA26_BB
4
3.804
-8.071
27.073
0.096
-0.433
3.442
35.164
A
A
7
8
1.000
B
B
25
24
3.450
0.604
0.111
-0.469
AA_DT7DT8:DA24DA25_BB
5
0.081
-0.134
35.159
-0.871
-0.171
3.224
37.149
A
A
8
9
5.711
B
B
24
23
3.191
3.632
0.498
0.355
AA_DT8DT9:DA23DA24_BB
6
1.202
-1.890
36.958
0.081
-0.624
3.231
37.170
A
A
9
10
2.284
B
B
23
22
3.177
1.454
-0.253
1.226
AA_DT9DA10:DT22DA23_BB
7
-2.862
4.495
37.036
1.733
0.022
3.334
32.458
A
A
10
11
1.137
B
B
22
21
3.340
0.636
-0.185
-0.484
AA_DA10DT11:DA21DT22_BB
8
-0.895
1.601
32.439
-0.980
0.171
3.681
44.537
A
A
11
12
4.559
B
B
21
20
3.630
3.452
0.409
0.963
AA_DT11DA12:DT20DA21_BB
9
-1.040
1.373
44.399
0.915
-0.646
2.738
31.390
A
A
12
13
-2.191
B
B
20
19
2.771
-1.182
0.156
-0.187
AA_DA12DA13:DT19DT20_BB
10
-3.833
7.103
31.139
-0.157
-0.896
3.371
37.180
A
A
13
14
4.530
B
B
19
18
3.432
2.886
-0.251
-0.716
AA_DA13DG14:DC18DT19_BB
11
-0.399
0.627
37.070
-1.523
0.338
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
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
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 T11C MUTANT
RCSB
Y
RCSB
2001-07-13
REL
REL
SYNTHETIC PEPTIDE
sample
1IJW
PDB
experimental model
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
T
9
n
8
DT
9
A
A
10
n
9
DA
10
A
T
11
n
10
DT
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
A
21
n
6
DA
21
B
T
22
n
7
DT
22
B
A
23
n
8
DA
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
n
1
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
ILE
185
n
47
ILE
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
CG
LYS
146
C
CG
LYS
8
1
Y
1
C
CD
LYS
146
C
CD
LYS
8
1
Y
1
C
CE
LYS
146
C
CE
LYS
8
1
Y
1
C
NZ
LYS
146
C
NZ
LYS
8
1
Y
1
C
CB
GLU
150
C
CB
GLU
12
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
ARG
154
C
CG
ARG
16
1
Y
1
C
CD
ARG
154
C
CD
ARG
16
1
Y
1
C
NE
ARG
154
C
NE
ARG
16
1
Y
1
C
CZ
ARG
154
C
CZ
ARG
16
1
Y
1
C
NH1
ARG
154
C
NH1
ARG
16
1
Y
1
C
NH2
ARG
154
C
NH2
ARG
16
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
CB
GLN
164
C
CB
GLN
26
1
Y
1
C
CD
GLN
164
C
CD
GLN
26
1
Y
1
C
OE1
GLN
164
C
OE1
GLN
26
1
Y
1
C
NE2
GLN
164
C
NE2
GLN
26
1
Y
1
C
GLY
139
C
GLY
1
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
C
C
O
OG
PRO
SER
181
184
2.18
1
A
DA
15
0.058
SIDE CHAIN
1
B
DA
23
0.058
SIDE CHAIN
1
B
DA
28
0.081
SIDE CHAIN
1
B
DC
29
0.069
SIDE CHAIN
1
-2.89
0.40
104.50
101.61
B
B
B
O4'
C4'
C3'
DA
DA
DA
16
16
16
A
N
1
12.36
1.20
115.70
128.06
B
B
B
C5'
C4'
C3'
DA
DA
DA
16
16
16
A
N
1
-14.68
1.80
114.10
99.42
B
B
B
C5'
C4'
C3'
DA
DA
DA
16
16
16
B
N
1
10.19
1.10
109.80
119.99
B
B
B
C5'
C4'
O4'
DT
DT
DT
17
17
17
A
A
N
1
15.39
2.00
112.30
127.69
B
B
B
C4'
C3'
O3'
DT
DT
DT
17
17
17
B
N
1
C
ARG
142
-40.65
156.61
1
C
ASN
145
-46.94
159.87
1
C
ARG
154
-60.78
-85.72
1
C
LEU
155
-23.55
-52.16
1
C
HIS
160
3.35
138.70
1
C
ARG
162
-49.59
1.52
1
C
SER
184
-169.74
39.41
PROTEIN_REP.PARAM
PROTEIN.TOP
DNA-RNA_REP.PARAM
DNA-RNA.TOP
53.10
17.368
0.00000
0.00000
3.275
0.00000
-20.643
0.3281000
0.2556000
0.2556000
2.86
41.30
362
3502
9.27
89.63
RANDOM
1
ANISOTROPIC_FIXED_ISOTROPIC
0.000
MOLECULAR REPLACEMENT
1IJW
MLF
100.00
0.35
0.46
0.43
5.00
0.38
0.46
2.86
41.30
0
930
0
576
354
0.009
1.592
20.222
1.842
5.16
4.000
7.51
6.000
7.43
6.000
10.31
7.000
0.3948000
0.3904000
2.99
43
343
8
9.00
80.76
44.00
2.86
41.3
1JKQ
3502
0.000
0.1880000
1
15.26
12.0
89.63
2.86
2.99
3.00
0.1880000
2.04
80.76
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
C
ASN
145
C
ASN
7
HELX_P
C
GLY
159
C
GLY
21
1
1
15
C
GLN
163
C
GLN
25
HELX_P
C
PHE
169
C
PHE
31
1
2
7
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
DT
9
A
N3
DT
8
1_555
B
DA
23
B
N1
DA
8
1_555
hydrog
WATSON-CRICK
A
DT
9
A
O4
DT
8
1_555
B
DA
23
B
N6
DA
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
DT
11
A
N3
DT
10
1_555
B
DA
21
B
N1
DA
6
1_555
hydrog
WATSON-CRICK
A
DT
11
A
O4
DT
10
1_555
B
DA
21
B
N6
DA
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, G9T MUTANT, DNA BINDING PROTEIN-DNA COMPLEX
HIN_SALTY
UNP
3
139
P03013
GRPRAINKHEQEQISRLLEKGHPRQQLAIIFGIGVSTLYRYFPASSIKKRMN
1JKQ
PDB
1
1JKQ
1JKQ
PDB
2
1JKQ
139
190
1JKQ
139
190
P03013
C
1
1
52
2
15
1JKQ
2
15
1JKQ
A
2
1
14
16
29
1JKQ
16
29
1JKQ
B
3
1
14
20
C 2 2 21