0.022967
0.000000
0.000000
0.000000
0.013701
0.000000
0.000000
0.000000
0.012768
0.00000
0.00000
0.00000
Muroya, A.
Tsuchiya, D.
Ishikawa, M.
Haruki, M.
Morikawa, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
43.540
72.990
78.320
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 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
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
O
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
N
N
94
N
C
N
95
N
C
N
96
N
O
N
97
N
O
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
N
N
104
S
C
N
105
N
C
N
106
N
O
N
107
N
C
Y
108
N
C
Y
109
N
N
Y
110
N
C
Y
111
N
C
Y
112
N
N
N
113
N
O
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
O
N
125
N
H
N
126
N
H
N
127
N
N
N
128
S
C
N
129
N
C
N
130
N
O
N
131
S
C
N
132
N
C
N
133
N
C
N
134
N
C
N
135
N
O
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
H
N
145
N
H
N
146
N
H
N
147
N
H
N
148
N
H
N
149
N
N
N
150
S
C
N
151
N
C
N
152
N
O
N
153
N
C
N
154
N
C
N
155
N
C
N
156
N
C
N
157
N
O
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
H
N
167
N
H
N
168
N
H
N
169
N
H
N
170
N
H
N
171
N
N
N
172
S
C
N
173
N
C
N
174
N
O
N
175
N
C
N
176
N
C
N
177
N
C
N
178
N
C
N
179
N
N
N
180
N
O
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
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
N
N
197
S
C
N
198
N
C
N
199
N
O
N
200
N
C
N
201
N
C
N
202
N
S
N
203
N
C
N
204
N
O
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
H
N
214
N
H
N
215
N
H
N
216
N
N
N
217
S
C
N
218
N
C
N
219
N
O
N
220
N
C
Y
221
N
C
Y
222
N
C
Y
223
N
C
Y
224
N
C
Y
225
N
C
Y
226
N
C
N
227
N
O
N
228
N
H
N
229
N
H
N
230
N
H
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
N
N
240
S
C
N
241
N
C
N
242
N
O
N
243
N
C
N
244
N
C
N
245
N
C
N
246
N
O
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
O
N
262
N
O
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
N
N
271
S
C
N
272
N
C
N
273
N
O
N
274
R
C
N
275
N
O
N
276
N
C
N
277
N
O
N
278
N
H
N
279
N
H
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
N
C
Y
292
N
C
Y
293
N
C
Y
294
N
C
Y
295
N
N
Y
296
N
C
Y
297
N
C
Y
298
N
C
Y
299
N
C
Y
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
N
N
315
S
C
N
316
N
C
N
317
N
O
N
318
N
C
Y
319
N
C
Y
320
N
C
Y
321
N
C
Y
322
N
C
Y
323
N
C
Y
324
N
C
N
325
N
O
N
326
N
O
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
N
N
339
S
C
N
340
N
C
N
341
N
O
N
342
N
C
N
343
N
C
N
344
N
C
N
345
N
O
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
H
N
356
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
doub
N
95
N
sing
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
Y
108
N
sing
Y
109
N
doub
Y
110
N
doub
N
111
N
sing
Y
112
N
sing
N
113
N
sing
Y
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
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
doub
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
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
doub
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
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
doub
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
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
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
sing
N
210
N
sing
N
211
N
doub
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
Y
216
N
doub
Y
217
N
sing
Y
218
N
sing
N
219
N
sing
Y
220
N
doub
N
221
N
sing
Y
222
N
doub
N
223
N
sing
Y
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
doub
N
235
N
sing
N
236
N
sing
N
237
N
sing
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
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
doub
N
265
N
sing
N
266
N
sing
N
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
sing
N
280
N
doub
N
281
N
sing
N
282
N
sing
N
283
N
sing
N
284
N
sing
Y
285
N
doub
Y
286
N
sing
Y
287
N
sing
N
288
N
sing
Y
289
N
doub
Y
290
N
sing
Y
291
N
sing
N
292
N
sing
Y
293
N
sing
Y
294
N
doub
N
295
N
sing
Y
296
N
doub
N
297
N
sing
Y
298
N
sing
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
doub
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
sing
Y
313
N
doub
Y
314
N
sing
Y
315
N
sing
N
316
N
sing
Y
317
N
doub
N
318
N
sing
Y
319
N
doub
N
320
N
sing
Y
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
doub
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
US
Protein Sci.
PRCIEI
0795
0961-8368
10
707
714
10.1110/ps.48001
11274461
Catalytic center of an archaeal type 2 ribonuclease H as revealed by X-ray crystallographic and mutational analyses.
2001
10.2210/pdb1io2/pdb
pdb_00001io2
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
MONOCHROMETER
IMAGE PLATE
1999-11-19
FUJI
SI
SINGLE WAVELENGTH
M
x-ray
1
1.0000
1.0
BL-6A
Photon Factory
1.0000
1.0000
SYNCHROTRON
PHOTON FACTORY BEAMLINE BL-6A
23974.449
RIBONUCLEASE HII
3.1.26.4
RESIDUES 1-213
1
man
polymer
18.015
water
216
nat
water
no
no
MKIAGIDEAGRGPVIGPMVIAAVVVDENSLPKLEELKVRDSKKLTPKRREKLFNEILGVLDDYVILELPPDVIGSREGTL
NEFEVENFAKALNSLKVKPDVIYADAADVDEERFARELGERLNFEAEVVAKHKADDIFPVVSAASILAKVTRDRAVEKLK
EEYGEIGSGYPSDPRTRAFLENYYREHGEFPPIVRKGWKTLKKIAEKVESEKK
MKIAGIDEAGRGPVIGPMVIAAVVVDENSLPKLEELKVRDSKKLTPKRREKLFNEILGVLDDYVILELPPDVIGSREGTL
NEFEVENFAKALNSLKVKPDVIYADAADVDEERFARELGERLNFEAEVVAKHKADDIFPVVSAASILAKVTRDRAVEKLK
EEYGEIGSGYPSDPRTRAFLENYYREHGEFPPIVRKGWKTLKKIAEKVESEKK
A
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
Thermococcus
Thermococcus kodakarensis
KOD1
Escherichia
sample
RNHB
69014
Thermococcus kodakarensis
562
Escherichia coli
HB101
PLASMID
PJAL700K
1
2.59
52.59
VAPOR DIFFUSION, HANGING DROP
6.50
PEG 6000, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
293.0
chem_comp_atom
chem_comp_bond
database_2
repository
Initial release
Version format compliance
Source and taxonomy
Version format compliance
Data collection
Database references
1
0
2001-04-18
1
1
2008-04-27
1
2
2011-07-13
1
3
2023-12-27
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
RCSB
Y
PDBJ
2000-12-28
REL
REL
HOH
water
WAT
301
2
HOH
HOH
301
A
WAT
302
2
HOH
HOH
302
A
WAT
303
2
HOH
HOH
303
A
WAT
304
2
HOH
HOH
304
A
WAT
305
2
HOH
HOH
305
A
WAT
306
2
HOH
HOH
306
A
WAT
307
2
HOH
HOH
307
A
WAT
308
2
HOH
HOH
308
A
WAT
309
2
HOH
HOH
309
A
WAT
310
2
HOH
HOH
310
A
WAT
311
2
HOH
HOH
311
A
WAT
312
2
HOH
HOH
312
A
WAT
313
2
HOH
HOH
313
A
WAT
314
2
HOH
HOH
314
A
WAT
315
2
HOH
HOH
315
A
WAT
316
2
HOH
HOH
316
A
WAT
317
2
HOH
HOH
317
A
WAT
318
2
HOH
HOH
318
A
WAT
319
2
HOH
HOH
319
A
WAT
320
2
HOH
HOH
320
A
WAT
321
2
HOH
HOH
321
A
WAT
322
2
HOH
HOH
322
A
WAT
323
2
HOH
HOH
323
A
WAT
324
2
HOH
HOH
324
A
WAT
325
2
HOH
HOH
325
A
WAT
326
2
HOH
HOH
326
A
WAT
327
2
HOH
HOH
327
A
WAT
328
2
HOH
HOH
328
A
WAT
329
2
HOH
HOH
329
A
WAT
330
2
HOH
HOH
330
A
WAT
331
2
HOH
HOH
331
A
WAT
332
2
HOH
HOH
332
A
WAT
333
2
HOH
HOH
333
A
WAT
334
2
HOH
HOH
334
A
WAT
335
2
HOH
HOH
335
A
WAT
336
2
HOH
HOH
336
A
WAT
337
2
HOH
HOH
337
A
WAT
338
2
HOH
HOH
338
A
WAT
339
2
HOH
HOH
339
A
WAT
340
2
HOH
HOH
340
A
WAT
341
2
HOH
HOH
341
A
WAT
342
2
HOH
HOH
342
A
WAT
343
2
HOH
HOH
343
A
WAT
344
2
HOH
HOH
344
A
WAT
345
2
HOH
HOH
345
A
WAT
346
2
HOH
HOH
346
A
WAT
347
2
HOH
HOH
347
A
WAT
348
2
HOH
HOH
348
A
WAT
349
2
HOH
HOH
349
A
WAT
350
2
HOH
HOH
350
A
WAT
351
2
HOH
HOH
351
A
WAT
352
2
HOH
HOH
352
A
WAT
353
2
HOH
HOH
353
A
WAT
354
2
HOH
HOH
354
A
WAT
355
2
HOH
HOH
355
A
WAT
356
2
HOH
HOH
356
A
WAT
357
2
HOH
HOH
357
A
WAT
358
2
HOH
HOH
358
A
WAT
359
2
HOH
HOH
359
A
WAT
360
2
HOH
HOH
360
A
WAT
361
2
HOH
HOH
361
A
WAT
362
2
HOH
HOH
362
A
WAT
363
2
HOH
HOH
363
A
WAT
364
2
HOH
HOH
364
A
WAT
365
2
HOH
HOH
365
A
WAT
366
2
HOH
HOH
366
A
WAT
367
2
HOH
HOH
367
A
WAT
368
2
HOH
HOH
368
A
WAT
369
2
HOH
HOH
369
A
WAT
370
2
HOH
HOH
370
A
WAT
371
2
HOH
HOH
371
A
WAT
372
2
HOH
HOH
372
A
WAT
373
2
HOH
HOH
373
A
WAT
374
2
HOH
HOH
374
A
WAT
375
2
HOH
HOH
375
A
WAT
376
2
HOH
HOH
376
A
WAT
377
2
HOH
HOH
377
A
WAT
378
2
HOH
HOH
378
A
WAT
379
2
HOH
HOH
379
A
WAT
380
2
HOH
HOH
380
A
WAT
381
2
HOH
HOH
381
A
WAT
382
2
HOH
HOH
382
A
WAT
383
2
HOH
HOH
383
A
WAT
384
2
HOH
HOH
384
A
WAT
385
2
HOH
HOH
385
A
WAT
386
2
HOH
HOH
386
A
WAT
387
2
HOH
HOH
387
A
WAT
388
2
HOH
HOH
388
A
WAT
389
2
HOH
HOH
389
A
WAT
390
2
HOH
HOH
390
A
WAT
391
2
HOH
HOH
391
A
WAT
392
2
HOH
HOH
392
A
WAT
393
2
HOH
HOH
393
A
WAT
394
2
HOH
HOH
394
A
WAT
395
2
HOH
HOH
395
A
WAT
396
2
HOH
HOH
396
A
WAT
397
2
HOH
HOH
397
A
WAT
398
2
HOH
HOH
398
A
WAT
399
2
HOH
HOH
399
A
WAT
400
2
HOH
HOH
400
A
WAT
401
2
HOH
HOH
401
A
WAT
402
2
HOH
HOH
402
A
WAT
403
2
HOH
HOH
403
A
WAT
404
2
HOH
HOH
404
A
WAT
405
2
HOH
HOH
405
A
WAT
406
2
HOH
HOH
406
A
WAT
407
2
HOH
HOH
407
A
WAT
408
2
HOH
HOH
408
A
WAT
409
2
HOH
HOH
409
A
WAT
410
2
HOH
HOH
410
A
WAT
411
2
HOH
HOH
411
A
WAT
412
2
HOH
HOH
412
A
WAT
413
2
HOH
HOH
413
A
WAT
414
2
HOH
HOH
414
A
WAT
415
2
HOH
HOH
415
A
WAT
416
2
HOH
HOH
416
A
WAT
417
2
HOH
HOH
417
A
WAT
418
2
HOH
HOH
418
A
WAT
419
2
HOH
HOH
419
A
WAT
420
2
HOH
HOH
420
A
WAT
421
2
HOH
HOH
421
A
WAT
422
2
HOH
HOH
422
A
WAT
423
2
HOH
HOH
423
A
WAT
424
2
HOH
HOH
424
A
WAT
425
2
HOH
HOH
425
A
WAT
426
2
HOH
HOH
426
A
WAT
427
2
HOH
HOH
427
A
WAT
428
2
HOH
HOH
428
A
WAT
429
2
HOH
HOH
429
A
WAT
430
2
HOH
HOH
430
A
WAT
431
2
HOH
HOH
431
A
WAT
432
2
HOH
HOH
432
A
WAT
433
2
HOH
HOH
433
A
WAT
434
2
HOH
HOH
434
A
WAT
435
2
HOH
HOH
435
A
WAT
436
2
HOH
HOH
436
A
WAT
437
2
HOH
HOH
437
A
WAT
438
2
HOH
HOH
438
A
WAT
439
2
HOH
HOH
439
A
WAT
440
2
HOH
HOH
440
A
WAT
441
2
HOH
HOH
441
A
WAT
442
2
HOH
HOH
442
A
WAT
443
2
HOH
HOH
443
A
WAT
444
2
HOH
HOH
444
A
WAT
445
2
HOH
HOH
445
A
WAT
446
2
HOH
HOH
446
A
WAT
447
2
HOH
HOH
447
A
WAT
448
2
HOH
HOH
448
A
WAT
449
2
HOH
HOH
449
A
WAT
450
2
HOH
HOH
450
A
WAT
451
2
HOH
HOH
451
A
WAT
452
2
HOH
HOH
452
A
WAT
453
2
HOH
HOH
453
A
WAT
454
2
HOH
HOH
454
A
WAT
455
2
HOH
HOH
455
A
WAT
456
2
HOH
HOH
456
A
WAT
457
2
HOH
HOH
457
A
WAT
458
2
HOH
HOH
458
A
WAT
459
2
HOH
HOH
459
A
WAT
460
2
HOH
HOH
460
A
WAT
461
2
HOH
HOH
461
A
WAT
462
2
HOH
HOH
462
A
WAT
463
2
HOH
HOH
463
A
WAT
464
2
HOH
HOH
464
A
WAT
465
2
HOH
HOH
465
A
WAT
466
2
HOH
HOH
466
A
WAT
467
2
HOH
HOH
467
A
WAT
468
2
HOH
HOH
468
A
WAT
469
2
HOH
HOH
469
A
WAT
470
2
HOH
HOH
470
A
WAT
471
2
HOH
HOH
471
A
WAT
472
2
HOH
HOH
472
A
WAT
473
2
HOH
HOH
473
A
WAT
474
2
HOH
HOH
474
A
WAT
475
2
HOH
HOH
475
A
WAT
476
2
HOH
HOH
476
A
WAT
477
2
HOH
HOH
477
A
WAT
478
2
HOH
HOH
478
A
WAT
479
2
HOH
HOH
479
A
WAT
480
2
HOH
HOH
480
A
WAT
481
2
HOH
HOH
481
A
WAT
482
2
HOH
HOH
482
A
WAT
483
2
HOH
HOH
483
A
WAT
484
2
HOH
HOH
484
A
WAT
485
2
HOH
HOH
485
A
WAT
486
2
HOH
HOH
486
A
WAT
487
2
HOH
HOH
487
A
WAT
488
2
HOH
HOH
488
A
WAT
489
2
HOH
HOH
489
A
WAT
490
2
HOH
HOH
490
A
WAT
491
2
HOH
HOH
491
A
WAT
492
2
HOH
HOH
492
A
WAT
493
2
HOH
HOH
493
A
WAT
494
2
HOH
HOH
494
A
WAT
495
2
HOH
HOH
495
A
WAT
496
2
HOH
HOH
496
A
WAT
497
2
HOH
HOH
497
A
WAT
498
2
HOH
HOH
498
A
WAT
499
2
HOH
HOH
499
A
WAT
500
2
HOH
HOH
500
A
WAT
501
2
HOH
HOH
501
A
WAT
502
2
HOH
HOH
502
A
WAT
503
2
HOH
HOH
503
A
WAT
504
2
HOH
HOH
504
A
WAT
505
2
HOH
HOH
505
A
WAT
506
2
HOH
HOH
506
A
WAT
507
2
HOH
HOH
507
A
WAT
508
2
HOH
HOH
508
A
WAT
509
2
HOH
HOH
509
A
WAT
510
2
HOH
HOH
510
A
WAT
511
2
HOH
HOH
511
A
WAT
512
2
HOH
HOH
512
A
WAT
513
2
HOH
HOH
513
A
WAT
514
2
HOH
HOH
514
A
WAT
515
2
HOH
HOH
515
A
WAT
516
2
HOH
HOH
516
A
MET
1
n
1
MET
1
A
LYS
2
n
2
LYS
2
A
ILE
3
n
3
ILE
3
A
ALA
4
n
4
ALA
4
A
GLY
5
n
5
GLY
5
A
ILE
6
n
6
ILE
6
A
ASP
7
n
7
ASP
7
A
GLU
8
n
8
GLU
8
A
ALA
9
n
9
ALA
9
A
GLY
10
n
10
GLY
10
A
ARG
11
n
11
ARG
11
A
GLY
12
n
12
GLY
12
A
PRO
13
n
13
PRO
13
A
VAL
14
n
14
VAL
14
A
ILE
15
n
15
ILE
15
A
GLY
16
n
16
GLY
16
A
PRO
17
n
17
PRO
17
A
MET
18
n
18
MET
18
A
VAL
19
n
19
VAL
19
A
ILE
20
n
20
ILE
20
A
ALA
21
n
21
ALA
21
A
ALA
22
n
22
ALA
22
A
VAL
23
n
23
VAL
23
A
VAL
24
n
24
VAL
24
A
VAL
25
n
25
VAL
25
A
ASP
26
n
26
ASP
26
A
GLU
27
n
27
GLU
27
A
ASN
28
n
28
ASN
28
A
SER
29
n
29
SER
29
A
LEU
30
n
30
LEU
30
A
PRO
31
n
31
PRO
31
A
LYS
32
n
32
LYS
32
A
LEU
33
n
33
LEU
33
A
GLU
34
n
34
GLU
34
A
GLU
35
n
35
GLU
35
A
LEU
36
n
36
LEU
36
A
LYS
37
n
37
LYS
37
A
VAL
38
n
38
VAL
38
A
ARG
39
n
39
ARG
39
A
ASP
40
n
40
ASP
40
A
SER
41
n
41
SER
41
A
LYS
42
n
42
LYS
42
A
LYS
43
n
43
LYS
43
A
LEU
44
n
44
LEU
44
A
THR
45
n
45
THR
45
A
PRO
46
n
46
PRO
46
A
LYS
47
n
47
LYS
47
A
ARG
48
n
48
ARG
48
A
ARG
49
n
49
ARG
49
A
GLU
50
n
50
GLU
50
A
LYS
51
n
51
LYS
51
A
LEU
52
n
52
LEU
52
A
PHE
53
n
53
PHE
53
A
ASN
54
n
54
ASN
54
A
GLU
55
n
55
GLU
55
A
ILE
56
n
56
ILE
56
A
LEU
57
n
57
LEU
57
A
GLY
58
n
58
GLY
58
A
VAL
59
n
59
VAL
59
A
LEU
60
n
60
LEU
60
A
ASP
61
n
61
ASP
61
A
ASP
62
n
62
ASP
62
A
TYR
63
n
63
TYR
63
A
VAL
64
n
64
VAL
64
A
ILE
65
n
65
ILE
65
A
LEU
66
n
66
LEU
66
A
GLU
67
n
67
GLU
67
A
LEU
68
n
68
LEU
68
A
PRO
69
n
69
PRO
69
A
PRO
70
n
70
PRO
70
A
ASP
71
n
71
ASP
71
A
VAL
72
n
72
VAL
72
A
ILE
73
n
73
ILE
73
A
GLY
74
n
74
GLY
74
A
SER
75
n
75
SER
75
A
ARG
76
n
76
ARG
76
A
GLU
77
n
77
GLU
77
A
GLY
78
n
78
GLY
78
A
THR
79
n
79
THR
79
A
LEU
80
n
80
LEU
80
A
ASN
81
n
81
ASN
81
A
GLU
82
n
82
GLU
82
A
PHE
83
n
83
PHE
83
A
GLU
84
n
84
GLU
84
A
VAL
85
n
85
VAL
85
A
GLU
86
n
86
GLU
86
A
ASN
87
n
87
ASN
87
A
PHE
88
n
88
PHE
88
A
ALA
89
n
89
ALA
89
A
LYS
90
n
90
LYS
90
A
ALA
91
n
91
ALA
91
A
LEU
92
n
92
LEU
92
A
ASN
93
n
93
ASN
93
A
SER
94
n
94
SER
94
A
LEU
95
n
95
LEU
95
A
LYS
96
n
96
LYS
96
A
VAL
97
n
97
VAL
97
A
LYS
98
n
98
LYS
98
A
PRO
99
n
99
PRO
99
A
ASP
100
n
100
ASP
100
A
VAL
101
n
101
VAL
101
A
ILE
102
n
102
ILE
102
A
TYR
103
n
103
TYR
103
A
ALA
104
n
104
ALA
104
A
ASP
105
n
105
ASP
105
A
ALA
106
n
106
ALA
106
A
ALA
107
n
107
ALA
107
A
ASP
108
n
108
ASP
108
A
VAL
109
n
109
VAL
109
A
ASP
110
n
110
ASP
110
A
GLU
111
n
111
GLU
111
A
GLU
112
n
112
GLU
112
A
ARG
113
n
113
ARG
113
A
PHE
114
n
114
PHE
114
A
ALA
115
n
115
ALA
115
A
ARG
116
n
116
ARG
116
A
GLU
117
n
117
GLU
117
A
LEU
118
n
118
LEU
118
A
GLY
119
n
119
GLY
119
A
GLU
120
n
120
GLU
120
A
ARG
121
n
121
ARG
121
A
LEU
122
n
122
LEU
122
A
ASN
123
n
123
ASN
123
A
PHE
124
n
124
PHE
124
A
GLU
125
n
125
GLU
125
A
ALA
126
n
126
ALA
126
A
GLU
127
n
127
GLU
127
A
VAL
128
n
128
VAL
128
A
VAL
129
n
129
VAL
129
A
ALA
130
n
130
ALA
130
A
LYS
131
n
131
LYS
131
A
HIS
132
n
132
HIS
132
A
LYS
133
n
133
LYS
133
A
ALA
134
n
134
ALA
134
A
ASP
135
n
135
ASP
135
A
ASP
136
n
136
ASP
136
A
ILE
137
n
137
ILE
137
A
PHE
138
n
138
PHE
138
A
PRO
139
n
139
PRO
139
A
VAL
140
n
140
VAL
140
A
VAL
141
n
141
VAL
141
A
SER
142
n
142
SER
142
A
ALA
143
n
143
ALA
143
A
ALA
144
n
144
ALA
144
A
SER
145
n
145
SER
145
A
ILE
146
n
146
ILE
146
A
LEU
147
n
147
LEU
147
A
ALA
148
n
148
ALA
148
A
LYS
149
n
149
LYS
149
A
VAL
150
n
150
VAL
150
A
THR
151
n
151
THR
151
A
ARG
152
n
152
ARG
152
A
ASP
153
n
153
ASP
153
A
ARG
154
n
154
ARG
154
A
ALA
155
n
155
ALA
155
A
VAL
156
n
156
VAL
156
A
GLU
157
n
157
GLU
157
A
LYS
158
n
158
LYS
158
A
LEU
159
n
159
LEU
159
A
LYS
160
n
160
LYS
160
A
GLU
161
n
161
GLU
161
A
GLU
162
n
162
GLU
162
A
TYR
163
n
163
TYR
163
A
GLY
164
n
164
GLY
164
A
GLU
165
n
165
GLU
165
A
ILE
166
n
166
ILE
166
A
GLY
167
n
167
GLY
167
A
SER
168
n
168
SER
168
A
GLY
169
n
169
GLY
169
A
TYR
170
n
170
TYR
170
A
PRO
171
n
171
PRO
171
A
SER
172
n
172
SER
172
A
ASP
173
n
173
ASP
173
A
PRO
174
n
174
PRO
174
A
ARG
175
n
175
ARG
175
A
THR
176
n
176
THR
176
A
ARG
177
n
177
ARG
177
A
ALA
178
n
178
ALA
178
A
PHE
179
n
179
PHE
179
A
LEU
180
n
180
LEU
180
A
GLU
181
n
181
GLU
181
A
ASN
182
n
182
ASN
182
A
TYR
183
n
183
TYR
183
A
TYR
184
n
184
TYR
184
A
ARG
185
n
185
ARG
185
A
GLU
186
n
186
GLU
186
A
HIS
187
n
187
HIS
187
A
GLY
188
n
188
GLY
188
A
GLU
189
n
189
GLU
189
A
PHE
190
n
190
PHE
190
A
PRO
191
n
191
PRO
191
A
PRO
192
n
192
PRO
192
A
ILE
193
n
193
ILE
193
A
VAL
194
n
194
VAL
194
A
ARG
195
n
195
ARG
195
A
LYS
196
n
196
LYS
196
A
GLY
197
n
197
GLY
197
A
TRP
198
n
198
TRP
198
A
LYS
199
n
199
LYS
199
A
THR
200
n
200
THR
200
A
LEU
201
n
201
LEU
201
A
LYS
202
n
202
LYS
202
A
LYS
203
n
203
LYS
203
A
ILE
204
n
204
ILE
204
A
ALA
205
n
205
ALA
205
A
GLU
206
n
206
GLU
206
A
LYS
207
n
207
LYS
207
A
VAL
208
n
208
VAL
208
A
GLU
209
n
209
GLU
209
A
SER
210
n
210
SER
210
A
GLU
211
n
211
GLU
211
A
LYS
212
n
212
LYS
212
A
LYS
213
n
213
LYS
213
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
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
N
LEU
68
A
N
LEU
68
A
O
MET
18
A
O
MET
18
A
O
VAL
25
A
O
VAL
25
A
N
ILE
3
A
N
ILE
3
A
N
ALA
4
A
N
ALA
4
A
O
VAL
101
A
O
VAL
101
A
N
ILE
102
A
N
ILE
102
A
O
GLU
127
A
O
GLU
127
1
A
CG
GLU
34
A
CG
GLU
34
1
Y
1
A
CD
GLU
34
A
CD
GLU
34
1
Y
1
A
OE1
GLU
34
A
OE1
GLU
34
1
Y
1
A
OE2
GLU
34
A
OE2
GLU
34
1
Y
1
A
CG
LYS
37
A
CG
LYS
37
1
Y
1
A
CD
LYS
37
A
CD
LYS
37
1
Y
1
A
CE
LYS
37
A
CE
LYS
37
1
Y
1
A
NZ
LYS
37
A
NZ
LYS
37
1
Y
1
A
CG
ARG
39
A
CG
ARG
39
1
Y
1
A
CD
ARG
39
A
CD
ARG
39
1
Y
1
A
NE
ARG
39
A
NE
ARG
39
1
Y
1
A
CZ
ARG
39
A
CZ
ARG
39
1
Y
1
A
NH1
ARG
39
A
NH1
ARG
39
1
Y
1
A
NH2
ARG
39
A
NH2
ARG
39
1
Y
1
A
CG
ASP
40
A
CG
ASP
40
1
Y
1
A
OD1
ASP
40
A
OD1
ASP
40
1
Y
1
A
OD2
ASP
40
A
OD2
ASP
40
1
Y
1
A
CG
LYS
43
A
CG
LYS
43
1
Y
1
A
CD
LYS
43
A
CD
LYS
43
1
Y
1
A
CE
LYS
43
A
CE
LYS
43
1
Y
1
A
NZ
LYS
43
A
NZ
LYS
43
1
Y
1
A
CG
LYS
158
A
CG
LYS
158
1
Y
1
A
CD
LYS
158
A
CD
LYS
158
1
Y
1
A
CE
LYS
158
A
CE
LYS
158
1
Y
1
A
NZ
LYS
158
A
NZ
LYS
158
1
Y
1
A
CG
LYS
196
A
CG
LYS
196
1
Y
1
A
CD
LYS
196
A
CD
LYS
196
1
Y
1
A
CE
LYS
196
A
CE
LYS
196
1
Y
1
A
NZ
LYS
196
A
NZ
LYS
196
1
Y
1
A
CG
LYS
202
A
CG
LYS
202
1
Y
1
A
CD
LYS
202
A
CD
LYS
202
1
Y
1
A
CE
LYS
202
A
CE
LYS
202
1
Y
1
A
NZ
LYS
202
A
NZ
LYS
202
1
Y
1
A
CG
LYS
213
A
CG
LYS
213
1
Y
1
A
CD
LYS
213
A
CD
LYS
213
1
Y
1
A
CE
LYS
213
A
CE
LYS
213
1
Y
1
A
NZ
LYS
213
A
NZ
LYS
213
1
Y
1
A
ASP
40
-106.19
51.86
1
A
PRO
192
-76.88
43.50
1
A
LYS
196
-38.18
-33.47
1
A
LYS
212
-22.76
129.66
PROTEIN_REP.PARAM
PROTEIN.TOP
WATER_REP.PARAM
WATER.TOP
22.80
0.150
0.0
0.0
-0.1396
0.0
1.246
0.2740000
0.2230000
0.2230000
2.00
15.00
1011
15068
14723
5.8
84.5
RANDOM
10000
1
ISOTROPIC
THROUGHOUT
2.000
MIR
ENGH & HUBER
FLAT MODEL
66.4
0.435
0.34
0.26
5.00
0.21
0.13
2.00
15.00
216
1868
0
0
1652
0.005
1.16
21.9
0.697
0.320
1.5
0.597
2.0
0.297
2.0
0.502
2.5
0.2750000
0.2180000
2.03
46
546
5.3
68.4
17.30
2.000
50.000
1IO2
52662
15205
0.0
0.000
0.0540000
1
17.8000
86.6
0.2540000
2.00
2.07
4.600
1
73.7
phasing
MLPHARE
refinement
CNS
data reduction
DENZO
data scaling
SCALEPACK
Crystal structure of type 2 ribonuclease h from hyperthermophilic archaeon, thermococcus kodakaraensis kod1
1
N
N
2
N
N
A
SER
29
A
SER
29
HELX_P
A
LEU
36
A
LEU
36
1
1
8
A
LYS
37
A
LYS
37
HELX_P
A
SER
41
A
SER
41
5
2
5
A
THR
45
A
THR
45
HELX_P
A
GLY
58
A
GLY
58
1
3
14
A
PRO
69
A
PRO
69
HELX_P
A
SER
75
A
SER
75
1
4
7
A
THR
79
A
THR
79
HELX_P
A
LEU
95
A
LEU
95
1
5
17
A
ASP
110
A
ASP
110
HELX_P
A
ARG
121
A
ARG
121
1
6
12
A
LYS
133
A
LYS
133
HELX_P
A
PHE
138
A
PHE
138
1
7
6
A
PHE
138
A
PHE
138
HELX_P
A
GLY
164
A
GLY
164
1
8
27
A
ASP
173
A
ASP
173
HELX_P
A
GLY
188
A
GLY
188
1
9
16
A
TRP
198
A
TRP
198
HELX_P
A
LYS
212
A
LYS
212
1
10
15
HYDROLASE
endonuclease, HYDROLASE
RNH2_PYRKO
UNP
1
O74035
1
213
1IO2
1
213
O74035
A
1
1
213
5
anti-parallel
anti-parallel
parallel
parallel
A
ASP
62
A
ASP
62
A
LEU
68
A
LEU
68
A
MET
18
A
MET
18
A
ASP
26
A
ASP
26
A
LYS
2
A
LYS
2
A
ALA
9
A
ALA
9
A
VAL
101
A
VAL
101
A
ASP
105
A
ASP
105
A
GLU
127
A
GLU
127
A
LYS
131
A
LYS
131
19
P 21 21 21