0.008123
0.000000
0.000000
0.000000
0.008123
0.000000
0.000000
0.000000
0.009042
0.00000
0.00000
0.00000
Han, S.
Bolin, J.T.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
16
90
90
90
123.1
123.1
110.6
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
Fe 2
55.845
FE (II) ION
non-polymer
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C7 H8 O2
124.137
3-METHYLCATECHOL
3-METHYL-BENZENE-1,2-DIOL
non-polymer
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 H10 O
74.122
TERTIARY-BUTYL ALCOHOL
2-METHYL-2-PROPANOL
non-polymer
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
R
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
S
N
80
N
O
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
FE
N
89
N
N
N
90
S
C
N
91
N
C
N
92
N
O
N
93
N
C
N
94
N
C
N
95
N
C
N
96
N
O
N
97
N
N
N
98
N
O
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
N
N
110
S
C
N
111
N
C
N
112
N
O
N
113
N
C
N
114
N
C
N
115
N
C
N
116
N
O
N
117
N
O
N
118
N
O
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
N
N
129
N
C
N
130
N
C
N
131
N
O
N
132
N
O
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
N
N
139
S
C
N
140
N
C
N
141
N
O
N
142
N
C
Y
143
N
C
Y
144
N
N
Y
145
N
C
Y
146
N
C
Y
147
N
N
N
148
N
O
N
149
N
H
N
150
N
H
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
O
N
160
N
H
N
161
N
H
N
162
N
N
N
163
S
C
N
164
N
C
N
165
N
O
N
166
S
C
N
167
N
C
N
168
N
C
N
169
N
C
N
170
N
O
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
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
N
N
185
S
C
N
186
N
C
N
187
N
O
N
188
N
C
N
189
N
C
N
190
N
C
N
191
N
C
N
192
N
O
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
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
H
N
206
N
N
N
207
S
C
N
208
N
C
N
209
N
O
N
210
N
C
N
211
N
C
N
212
N
C
N
213
N
C
N
214
N
N
N
215
N
O
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
H
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
Y
231
N
C
N
232
N
O
Y
233
N
C
N
234
N
O
Y
235
N
C
N
236
N
C
Y
237
N
C
Y
238
N
C
Y
239
N
C
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
N
N
249
S
C
N
250
N
C
N
251
N
O
N
252
N
C
N
253
N
C
N
254
N
S
N
255
N
C
N
256
N
O
N
257
N
H
N
258
N
H
N
259
N
H
N
260
N
H
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
N
N
269
S
C
N
270
N
C
N
271
N
O
N
272
N
C
Y
273
N
C
Y
274
N
C
Y
275
N
C
Y
276
N
C
Y
277
N
C
Y
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
N
N
292
S
C
N
293
N
C
N
294
N
O
N
295
N
C
N
296
N
C
N
297
N
C
N
298
N
O
N
299
N
H
N
300
N
H
N
301
N
H
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
N
N
309
S
C
N
310
N
C
N
311
N
O
N
312
N
C
N
313
N
O
N
314
N
O
N
315
N
H
N
316
N
H
N
317
N
H
N
318
N
H
N
319
N
H
N
320
N
H
N
321
N
H
N
322
N
O
N
323
N
C
N
324
N
C
N
325
N
C
N
326
N
C
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
N
N
338
S
C
N
339
N
C
N
340
N
O
N
341
R
C
N
342
N
O
N
343
N
C
N
344
N
O
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
N
N
355
S
C
N
356
N
C
N
357
N
O
N
358
N
C
Y
359
N
C
Y
360
N
C
Y
361
N
C
Y
362
N
N
Y
363
N
C
Y
364
N
C
Y
365
N
C
Y
366
N
C
Y
367
N
C
N
368
N
O
N
369
N
H
N
370
N
H
N
371
N
H
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
N
N
382
S
C
N
383
N
C
N
384
N
O
N
385
N
C
Y
386
N
C
Y
387
N
C
Y
388
N
C
Y
389
N
C
Y
390
N
C
Y
391
N
C
N
392
N
O
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
H
N
404
N
H
N
405
N
N
N
406
S
C
N
407
N
C
N
408
N
O
N
409
N
C
N
410
N
C
N
411
N
C
N
412
N
O
N
413
N
H
N
414
N
H
N
415
N
H
N
416
N
H
N
417
N
H
N
418
N
H
N
419
N
H
N
420
N
H
N
421
N
H
N
422
N
H
N
423
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
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
doub
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
doub
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
doub
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
doub
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
doub
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
Y
140
N
sing
Y
141
N
doub
Y
142
N
doub
N
143
N
sing
Y
144
N
sing
N
145
N
sing
Y
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
doub
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
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
doub
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
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
doub
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
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
Y
219
N
doub
Y
220
N
sing
N
221
N
sing
N
222
N
sing
Y
223
N
sing
N
224
N
sing
N
225
N
sing
Y
226
N
doub
N
227
N
sing
N
228
N
sing
N
229
N
sing
Y
230
N
sing
N
231
N
sing
Y
232
N
doub
N
233
N
sing
N
234
N
sing
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
doub
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
sing
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
doub
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
Y
265
N
doub
Y
266
N
sing
Y
267
N
sing
N
268
N
sing
Y
269
N
doub
N
270
N
sing
Y
271
N
doub
N
272
N
sing
Y
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
sing
N
282
N
sing
N
283
N
doub
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
sing
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
doub
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
Y
348
N
doub
Y
349
N
sing
Y
350
N
sing
N
351
N
sing
Y
352
N
doub
Y
353
N
sing
Y
354
N
sing
N
355
N
sing
Y
356
N
sing
Y
357
N
doub
N
358
N
sing
Y
359
N
doub
N
360
N
sing
Y
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
sing
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
sing
N
370
N
sing
N
371
N
doub
N
372
N
sing
N
373
N
sing
N
374
N
sing
N
375
N
sing
Y
376
N
doub
Y
377
N
sing
Y
378
N
sing
N
379
N
sing
Y
380
N
doub
N
381
N
sing
Y
382
N
doub
N
383
N
sing
Y
384
N
sing
N
385
N
sing
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
doub
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
sing
N
405
N
sing
N
406
N
sing
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
273
34887
34895
10.1074/jbc.273.52.34887
9857017
Molecular basis for the stabilization and inhibition of 2, 3-dihydroxybiphenyl 1,2-dioxygenase by t-butanol.
1998
US
Science
SCIEAS
0038
0036-8075
270
976
980
Crystal Structure of the Biphenyl-cleaving Extradiol Dioxygenase from a PCB-degrading Pseudomonad.
1995
John Wiley and Sons
UK
Handbook of Metalloproteins
0-471-62743-7
632
642
2,3-Dihydroxybiphenyl 1,2-dioxygenase.
2001
10.2210/pdb1knf/pdb
pdb_00001knf
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
298
1
mirrors
IMAGE PLATE
1995-11-30
RIGAKU RAXIS II
YALE MIRRORS
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU RU200
32377.598
2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE
1.13.11.39
1
man
polymer
55.845
FE (II) ION
2
syn
non-polymer
124.137
3-METHYLCATECHOL
1
syn
non-polymer
74.122
TERTIARY-BUTYL ALCOHOL
2
syn
non-polymer
18.015
water
121
nat
water
Biphenyl-2,3-diol 1,2-dioxygenase, DHBD
no
no
SIRSLGYMGFAVSDVAAWRSFLTQKLGLMEAGTTDNGDLFRIDSRAWRIAVQQGEVDDLAFAGYEVADAAGLAQMADKLK
QAGIAVTTGDASLARRRGVTGLITFADPFGLPLEIYYGASEVFEKPFLPGAAVSGFLTGEQGLGHFVRCVPDSDKALAFY
TDVLGFQLSDVIDMKMGPDVTVPAYFLHCNERHHTLAIAAFPLPKRIHHFMLEVASLDDVGFAFDRVDADGLITSTLGRH
TNDHMVSFYASTPSGVEVEYGWSARTVDRSWVVVRHDSPSMWGHKSVRDKAAARNKA
SIRSLGYMGFAVSDVAAWRSFLTQKLGLMEAGTTDNGDLFRIDSRAWRIAVQQGEVDDLAFAGYEVADAAGLAQMADKLK
QAGIAVTTGDASLARRRGVTGLITFADPFGLPLEIYYGASEVFEKPFLPGAAVSGFLTGEQGLGHFVRCVPDSDKALAFY
TDVLGFQLSDVIDMKMGPDVTVPAYFLHCNERHHTLAIAAFPLPKRIHHFMLEVASLDDVGFAFDRVDADGLITSTLGRH
TNDHMVSFYASTPSGVEVEYGWSARTVDRSWVVVRHDSPSMWGHKSVRDKAAARNKA
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Burkholderia
Burkholderia xenovorans
LB400
Burkholderia
sample
HYPEREXPRESSED IN THE PARENT STRAIN (This organism has been reclassified. Prior publications may refer to this source as Pseudomonas sp. strain LB400.)
BPHC
266265
Burkholderia xenovorans
292
Burkholderia cepacia
PLASMID
PLEBD4
1
3.22
62
VAPOR DIFFUSION, SITTING DROP
7.5
PEG4000, t-butanol, 3-methyl catechol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K
278
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
pdbx_struct_conn_angle
struct_conn
struct_site
repository
Initial release
Version format compliance
Derived calculations
Source and taxonomy
Version format compliance
Data collection
Database references
Derived calculations
Refinement description
1
0
2002-03-27
1
1
2008-04-27
1
2
2011-07-13
1
3
2023-08-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
1HAN is the same protein without substrate.
1KMY IS the Crystal Structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase Complexed with 2,3-dihydroxybiphenyl under Anaerobic Condition.
1KND IS the Crystal Structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase Complexed with Catechol under Anaerobic Condition.
RCSB
Y
RCSB
2001-12-18
REL
FE2
FE (II) ION
MBD
3-METHYLCATECHOL
TBU
TERTIARY-BUTYL ALCOHOL
HOH
water
1HAN
PDB
experimental model
FE2
500
2
FE2
FE2
500
A
FE2
501
2
FE2
FE2
501
A
MBD
301
3
MBD
MBD
301
A
TBU
601
4
TBU
TBU
601
A
TBU
600
4
TBU
TBU
600
A
HOH
1001
5
HOH
HOH
1001
A
HOH
1004
5
HOH
HOH
1004
A
HOH
1006
5
HOH
HOH
1006
A
HOH
1008
5
HOH
HOH
1008
A
HOH
1010
5
HOH
HOH
1010
A
HOH
1011
5
HOH
HOH
1011
A
HOH
1015
5
HOH
HOH
1015
A
HOH
1017
5
HOH
HOH
1017
A
HOH
1019
5
HOH
HOH
1019
A
HOH
1021
5
HOH
HOH
1021
A
HOH
1022
5
HOH
HOH
1022
A
HOH
1023
5
HOH
HOH
1023
A
HOH
1027
5
HOH
HOH
1027
A
HOH
1032
5
HOH
HOH
1032
A
HOH
1034
5
HOH
HOH
1034
A
HOH
1035
5
HOH
HOH
1035
A
HOH
1037
5
HOH
HOH
1037
A
HOH
1038
5
HOH
HOH
1038
A
HOH
1041
5
HOH
HOH
1041
A
HOH
1042
5
HOH
HOH
1042
A
HOH
1044
5
HOH
HOH
1044
A
HOH
1048
5
HOH
HOH
1048
A
HOH
1049
5
HOH
HOH
1049
A
HOH
1051
5
HOH
HOH
1051
A
HOH
1054
5
HOH
HOH
1054
A
HOH
1056
5
HOH
HOH
1056
A
HOH
1059
5
HOH
HOH
1059
A
HOH
1062
5
HOH
HOH
1062
A
HOH
1063
5
HOH
HOH
1063
A
HOH
1066
5
HOH
HOH
1066
A
HOH
1070
5
HOH
HOH
1070
A
HOH
1075
5
HOH
HOH
1075
A
HOH
1077
5
HOH
HOH
1077
A
HOH
2004
5
HOH
HOH
2004
A
HOH
2005
5
HOH
HOH
2005
A
HOH
2007
5
HOH
HOH
2007
A
HOH
2010
5
HOH
HOH
2010
A
HOH
2018
5
HOH
HOH
2018
A
HOH
2021
5
HOH
HOH
2021
A
HOH
2024
5
HOH
HOH
2024
A
HOH
3001
5
HOH
HOH
3001
A
HOH
3012
5
HOH
HOH
3012
A
HOH
4001
5
HOH
HOH
4001
A
HOH
4003
5
HOH
HOH
4003
A
HOH
4006
5
HOH
HOH
4006
A
HOH
4007
5
HOH
HOH
4007
A
HOH
4014
5
HOH
HOH
4014
A
HOH
4020
5
HOH
HOH
4020
A
HOH
4023
5
HOH
HOH
4023
A
HOH
4026
5
HOH
HOH
4026
A
HOH
4027
5
HOH
HOH
4027
A
HOH
5001
5
HOH
HOH
5001
A
HOH
5016
5
HOH
HOH
5016
A
HOH
5020
5
HOH
HOH
5020
A
HOH
5022
5
HOH
HOH
5022
A
HOH
5027
5
HOH
HOH
5027
A
HOH
5029
5
HOH
HOH
5029
A
HOH
5032
5
HOH
HOH
5032
A
HOH
5036
5
HOH
HOH
5036
A
HOH
5039
5
HOH
HOH
5039
A
HOH
5042
5
HOH
HOH
5042
A
HOH
5043
5
HOH
HOH
5043
A
HOH
5053
5
HOH
HOH
5053
A
HOH
5061
5
HOH
HOH
5061
A
HOH
5065
5
HOH
HOH
5065
A
HOH
5071
5
HOH
HOH
5071
A
HOH
5077
5
HOH
HOH
5077
A
HOH
5082
5
HOH
HOH
5082
A
HOH
5088
5
HOH
HOH
5088
A
HOH
5091
5
HOH
HOH
5091
A
HOH
5107
5
HOH
HOH
5107
A
HOH
5123
5
HOH
HOH
5123
A
HOH
5137
5
HOH
HOH
5137
A
HOH
6016
5
HOH
HOH
6016
A
HOH
6023
5
HOH
HOH
6023
A
HOH
6033
5
HOH
HOH
6033
A
HOH
6044
5
HOH
HOH
6044
A
HOH
6061
5
HOH
HOH
6061
A
HOH
6065
5
HOH
HOH
6065
A
HOH
6068
5
HOH
HOH
6068
A
HOH
6072
5
HOH
HOH
6072
A
HOH
6092
5
HOH
HOH
6092
A
HOH
6095
5
HOH
HOH
6095
A
HOH
6103
5
HOH
HOH
6103
A
HOH
6141
5
HOH
HOH
6141
A
HOH
6144
5
HOH
HOH
6144
A
HOH
6152
5
HOH
HOH
6152
A
HOH
6198
5
HOH
HOH
6198
A
HOH
7012
5
HOH
HOH
7012
A
HOH
7053
5
HOH
HOH
7053
A
HOH
7109
5
HOH
HOH
7109
A
HOH
7119
5
HOH
HOH
7119
A
HOH
7140
5
HOH
HOH
7140
A
HOH
7168
5
HOH
HOH
7168
A
HOH
7241
5
HOH
HOH
7241
A
HOH
8001
5
HOH
HOH
8001
A
HOH
8002
5
HOH
HOH
8002
A
HOH
8003
5
HOH
HOH
8003
A
HOH
8004
5
HOH
HOH
8004
A
HOH
8008
5
HOH
HOH
8008
A
HOH
8011
5
HOH
HOH
8011
A
HOH
8015
5
HOH
HOH
8015
A
HOH
8016
5
HOH
HOH
8016
A
HOH
8018
5
HOH
HOH
8018
A
HOH
8019
5
HOH
HOH
8019
A
HOH
8020
5
HOH
HOH
8020
A
HOH
8021
5
HOH
HOH
8021
A
HOH
8022
5
HOH
HOH
8022
A
HOH
8023
5
HOH
HOH
8023
A
HOH
8024
5
HOH
HOH
8024
A
HOH
8025
5
HOH
HOH
8025
A
HOH
8029
5
HOH
HOH
8029
A
HOH
8031
5
HOH
HOH
8031
A
HOH
8032
5
HOH
HOH
8032
A
HOH
8034
5
HOH
HOH
8034
A
HOH
8035
5
HOH
HOH
8035
A
HOH
8036
5
HOH
HOH
8036
A
HOH
8037
5
HOH
HOH
8037
A
HOH
9001
5
HOH
HOH
9001
A
HOH
9002
5
HOH
HOH
9002
A
HOH
9003
5
HOH
HOH
9003
A
SER
2
n
1
SER
2
A
ILE
3
n
2
ILE
3
A
ARG
4
n
3
ARG
4
A
SER
5
n
4
SER
5
A
LEU
6
n
5
LEU
6
A
GLY
7
n
6
GLY
7
A
TYR
8
n
7
TYR
8
A
MET
9
n
8
MET
9
A
GLY
10
n
9
GLY
10
A
PHE
11
n
10
PHE
11
A
ALA
12
n
11
ALA
12
A
VAL
13
n
12
VAL
13
A
SER
14
n
13
SER
14
A
ASP
15
n
14
ASP
15
A
VAL
16
n
15
VAL
16
A
ALA
17
n
16
ALA
17
A
ALA
18
n
17
ALA
18
A
TRP
19
n
18
TRP
19
A
ARG
20
n
19
ARG
20
A
SER
21
n
20
SER
21
A
PHE
22
n
21
PHE
22
A
LEU
23
n
22
LEU
23
A
THR
24
n
23
THR
24
A
GLN
25
n
24
GLN
25
A
LYS
26
n
25
LYS
26
A
LEU
27
n
26
LEU
27
A
GLY
28
n
27
GLY
28
A
LEU
29
n
28
LEU
29
A
MET
30
n
29
MET
30
A
GLU
31
n
30
GLU
31
A
ALA
32
n
31
ALA
32
A
GLY
33
n
32
GLY
33
A
THR
34
n
33
THR
34
A
THR
35
n
34
THR
35
A
ASP
36
n
35
ASP
36
A
ASN
37
n
36
ASN
37
A
GLY
38
n
37
GLY
38
A
ASP
39
n
38
ASP
39
A
LEU
40
n
39
LEU
40
A
PHE
41
n
40
PHE
41
A
ARG
42
n
41
ARG
42
A
ILE
43
n
42
ILE
43
A
ASP
44
n
43
ASP
44
A
SER
45
n
44
SER
45
A
ARG
46
n
45
ARG
46
A
ALA
47
n
46
ALA
47
A
TRP
48
n
47
TRP
48
A
ARG
49
n
48
ARG
49
A
ILE
50
n
49
ILE
50
A
ALA
51
n
50
ALA
51
A
VAL
52
n
51
VAL
52
A
GLN
53
n
52
GLN
53
A
GLN
54
n
53
GLN
54
A
GLY
55
n
54
GLY
55
A
GLU
56
n
55
GLU
56
A
VAL
57
n
56
VAL
57
A
ASP
58
n
57
ASP
58
A
ASP
59
n
58
ASP
59
A
LEU
60
n
59
LEU
60
A
ALA
61
n
60
ALA
61
A
PHE
62
n
61
PHE
62
A
ALA
63
n
62
ALA
63
A
GLY
64
n
63
GLY
64
A
TYR
65
n
64
TYR
65
A
GLU
66
n
65
GLU
66
A
VAL
67
n
66
VAL
67
A
ALA
68
n
67
ALA
68
A
ASP
69
n
68
ASP
69
A
ALA
70
n
69
ALA
70
A
ALA
71
n
70
ALA
71
A
GLY
72
n
71
GLY
72
A
LEU
73
n
72
LEU
73
A
ALA
74
n
73
ALA
74
A
GLN
75
n
74
GLN
75
A
MET
76
n
75
MET
76
A
ALA
77
n
76
ALA
77
A
ASP
78
n
77
ASP
78
A
LYS
79
n
78
LYS
79
A
LEU
80
n
79
LEU
80
A
LYS
81
n
80
LYS
81
A
GLN
82
n
81
GLN
82
A
ALA
83
n
82
ALA
83
A
GLY
84
n
83
GLY
84
A
ILE
85
n
84
ILE
85
A
ALA
86
n
85
ALA
86
A
VAL
87
n
86
VAL
87
A
THR
88
n
87
THR
88
A
THR
89
n
88
THR
89
A
GLY
90
n
89
GLY
90
A
ASP
91
n
90
ASP
91
A
ALA
92
n
91
ALA
92
A
SER
93
n
92
SER
93
A
LEU
94
n
93
LEU
94
A
ALA
95
n
94
ALA
95
A
ARG
96
n
95
ARG
96
A
ARG
97
n
96
ARG
97
A
ARG
98
n
97
ARG
98
A
GLY
99
n
98
GLY
99
A
VAL
100
n
99
VAL
100
A
THR
101
n
100
THR
101
A
GLY
102
n
101
GLY
102
A
LEU
103
n
102
LEU
103
A
ILE
104
n
103
ILE
104
A
THR
105
n
104
THR
105
A
PHE
106
n
105
PHE
106
A
ALA
107
n
106
ALA
107
A
ASP
108
n
107
ASP
108
A
PRO
109
n
108
PRO
109
A
PHE
110
n
109
PHE
110
A
GLY
111
n
110
GLY
111
A
LEU
112
n
111
LEU
112
A
PRO
113
n
112
PRO
113
A
LEU
114
n
113
LEU
114
A
GLU
115
n
114
GLU
115
A
ILE
116
n
115
ILE
116
A
TYR
117
n
116
TYR
117
A
TYR
118
n
117
TYR
118
A
GLY
119
n
118
GLY
119
A
ALA
120
n
119
ALA
120
A
SER
121
n
120
SER
121
A
GLU
122
n
121
GLU
122
A
VAL
123
n
122
VAL
123
A
PHE
124
n
123
PHE
124
A
GLU
125
n
124
GLU
125
A
LYS
126
n
125
LYS
126
A
PRO
127
n
126
PRO
127
A
PHE
128
n
127
PHE
128
A
LEU
129
n
128
LEU
129
A
PRO
130
n
129
PRO
130
A
GLY
131
n
130
GLY
131
A
ALA
132
n
131
ALA
132
A
ALA
133
n
132
ALA
133
A
VAL
134
n
133
VAL
134
A
SER
135
n
134
SER
135
A
GLY
136
n
135
GLY
136
A
PHE
137
n
136
PHE
137
A
LEU
138
n
137
LEU
138
A
THR
139
n
138
THR
139
A
GLY
140
n
139
GLY
140
A
GLU
141
n
140
GLU
141
A
GLN
142
n
141
GLN
142
A
GLY
143
n
142
GLY
143
A
LEU
144
n
143
LEU
144
A
GLY
145
n
144
GLY
145
A
HIS
146
n
145
HIS
146
A
PHE
147
n
146
PHE
147
A
VAL
148
n
147
VAL
148
A
ARG
149
n
148
ARG
149
A
CYS
150
n
149
CYS
150
A
VAL
151
n
150
VAL
151
A
PRO
152
n
151
PRO
152
A
ASP
153
n
152
ASP
153
A
SER
154
n
153
SER
154
A
ASP
155
n
154
ASP
155
A
LYS
156
n
155
LYS
156
A
ALA
157
n
156
ALA
157
A
LEU
158
n
157
LEU
158
A
ALA
159
n
158
ALA
159
A
PHE
160
n
159
PHE
160
A
TYR
161
n
160
TYR
161
A
THR
162
n
161
THR
162
A
ASP
163
n
162
ASP
163
A
VAL
164
n
163
VAL
164
A
LEU
165
n
164
LEU
165
A
GLY
166
n
165
GLY
166
A
PHE
167
n
166
PHE
167
A
GLN
168
n
167
GLN
168
A
LEU
169
n
168
LEU
169
A
SER
170
n
169
SER
170
A
ASP
171
n
170
ASP
171
A
VAL
172
n
171
VAL
172
A
ILE
173
n
172
ILE
173
A
ASP
174
n
173
ASP
174
A
MET
175
n
174
MET
175
A
LYS
176
n
175
LYS
176
A
MET
177
n
176
MET
177
A
GLY
178
n
177
GLY
178
A
PRO
179
n
178
PRO
179
A
ASP
180
n
179
ASP
180
A
VAL
181
n
180
VAL
181
A
THR
182
n
181
THR
182
A
VAL
183
n
182
VAL
183
A
PRO
184
n
183
PRO
184
A
ALA
185
n
184
ALA
185
A
TYR
186
n
185
TYR
186
A
PHE
187
n
186
PHE
187
A
LEU
188
n
187
LEU
188
A
HIS
189
n
188
HIS
189
A
CYS
190
n
189
CYS
190
A
ASN
191
n
190
ASN
191
A
GLU
192
n
191
GLU
192
A
ARG
193
n
192
ARG
193
A
HIS
194
n
193
HIS
194
A
HIS
195
n
194
HIS
195
A
THR
196
n
195
THR
196
A
LEU
197
n
196
LEU
197
A
ALA
198
n
197
ALA
198
A
ILE
199
n
198
ILE
199
A
ALA
200
n
199
ALA
200
A
ALA
201
n
200
ALA
201
A
PHE
202
n
201
PHE
202
A
PRO
203
n
202
PRO
203
A
LEU
204
n
203
LEU
204
A
PRO
205
n
204
PRO
205
A
LYS
206
n
205
LYS
206
A
ARG
207
n
206
ARG
207
A
ILE
208
n
207
ILE
208
A
HIS
209
n
208
HIS
209
A
HIS
210
n
209
HIS
210
A
PHE
211
n
210
PHE
211
A
MET
212
n
211
MET
212
A
LEU
213
n
212
LEU
213
A
GLU
214
n
213
GLU
214
A
VAL
215
n
214
VAL
215
A
ALA
216
n
215
ALA
216
A
SER
217
n
216
SER
217
A
LEU
218
n
217
LEU
218
A
ASP
219
n
218
ASP
219
A
ASP
220
n
219
ASP
220
A
VAL
221
n
220
VAL
221
A
GLY
222
n
221
GLY
222
A
PHE
223
n
222
PHE
223
A
ALA
224
n
223
ALA
224
A
PHE
225
n
224
PHE
225
A
ASP
226
n
225
ASP
226
A
ARG
227
n
226
ARG
227
A
VAL
228
n
227
VAL
228
A
ASP
229
n
228
ASP
229
A
ALA
230
n
229
ALA
230
A
ASP
231
n
230
ASP
231
A
GLY
232
n
231
GLY
232
A
LEU
233
n
232
LEU
233
A
ILE
234
n
233
ILE
234
A
THR
235
n
234
THR
235
A
SER
236
n
235
SER
236
A
THR
237
n
236
THR
237
A
LEU
238
n
237
LEU
238
A
GLY
239
n
238
GLY
239
A
ARG
240
n
239
ARG
240
A
HIS
241
n
240
HIS
241
A
THR
242
n
241
THR
242
A
ASN
243
n
242
ASN
243
A
ASP
244
n
243
ASP
244
A
HIS
245
n
244
HIS
245
A
MET
246
n
245
MET
246
A
VAL
247
n
246
VAL
247
A
SER
248
n
247
SER
248
A
PHE
249
n
248
PHE
249
A
TYR
250
n
249
TYR
250
A
ALA
251
n
250
ALA
251
A
SER
252
n
251
SER
252
A
THR
253
n
252
THR
253
A
PRO
254
n
253
PRO
254
A
SER
255
n
254
SER
255
A
GLY
256
n
255
GLY
256
A
VAL
257
n
256
VAL
257
A
GLU
258
n
257
GLU
258
A
VAL
259
n
258
VAL
259
A
GLU
260
n
259
GLU
260
A
TYR
261
n
260
TYR
261
A
GLY
262
n
261
GLY
262
A
TRP
263
n
262
TRP
263
A
SER
264
n
263
SER
264
A
ALA
265
n
264
ALA
265
A
ARG
266
n
265
ARG
266
A
THR
267
n
266
THR
267
A
VAL
268
n
267
VAL
268
A
ASP
269
n
268
ASP
269
A
ARG
270
n
269
ARG
270
A
SER
271
n
270
SER
271
A
TRP
272
n
271
TRP
272
A
VAL
273
n
272
VAL
273
A
VAL
274
n
273
VAL
274
A
VAL
275
n
274
VAL
275
A
ARG
276
n
275
ARG
276
A
HIS
277
n
276
HIS
277
A
ASP
278
n
277
ASP
278
A
SER
279
n
278
SER
279
A
PRO
280
n
279
PRO
280
A
SER
281
n
280
SER
281
A
MET
282
n
281
MET
282
A
TRP
283
n
282
TRP
283
A
GLY
284
n
283
GLY
284
A
HIS
285
n
284
HIS
285
A
LYS
286
n
285
LYS
286
A
SER
287
n
286
SER
287
A
VAL
288
n
287
VAL
288
A
ARG
289
n
288
ARG
289
A
n
289
290
A
n
290
291
A
n
291
292
A
n
292
293
A
n
293
294
A
n
294
295
A
n
295
296
A
n
296
297
A
n
297
298
A
author_and_software_defined_assembly
PISA,PQS
8
octameric
26660
-215
78170
A
HIS
146
A
NE2
HIS
145
1_555
A
FE2
500
B
FE
FE2
1_555
A
HIS
210
A
NE2
HIS
209
1_555
102.7
A
HIS
146
A
NE2
HIS
145
1_555
A
FE2
500
B
FE
FE2
1_555
A
GLU
260
A
OE2
GLU
259
1_555
106.3
A
HIS
210
A
NE2
HIS
209
1_555
A
FE2
500
B
FE
FE2
1_555
A
GLU
260
A
OE2
GLU
259
1_555
90.7
A
HIS
146
A
NE2
HIS
145
1_555
A
FE2
500
B
FE
FE2
1_555
A
MBD
301
A
D
OA1
MBD
1_555
103.8
A
HIS
210
A
NE2
HIS
209
1_555
A
FE2
500
B
FE
FE2
1_555
A
MBD
301
A
D
OA1
MBD
1_555
146.2
A
GLU
260
A
OE2
GLU
259
1_555
A
FE2
500
B
FE
FE2
1_555
A
MBD
301
A
D
OA1
MBD
1_555
101.6
A
HIS
146
A
NE2
HIS
145
1_555
A
FE2
500
B
FE
FE2
1_555
A
MBD
301
A
D
OA2
MBD
1_555
150.6
A
HIS
210
A
NE2
HIS
209
1_555
A
FE2
500
B
FE
FE2
1_555
A
MBD
301
A
D
OA2
MBD
1_555
77.3
A
GLU
260
A
OE2
GLU
259
1_555
A
FE2
500
B
FE
FE2
1_555
A
MBD
301
A
D
OA2
MBD
1_555
103.1
A
MBD
301
A
D
OA1
MBD
1_555
A
FE2
500
B
FE
FE2
1_555
A
MBD
301
A
D
OA2
MBD
1_555
69.3
A
HIS
146
A
NE2
HIS
145
1_555
A
FE2
500
B
FE
FE2
1_555
A
HOH
3001
B
G
O
HOH
1_555
92.2
A
HIS
210
A
NE2
HIS
209
1_555
A
FE2
500
B
FE
FE2
1_555
A
HOH
3001
B
G
O
HOH
1_555
163.3
A
GLU
260
A
OE2
GLU
259
1_555
A
FE2
500
B
FE
FE2
1_555
A
HOH
3001
B
G
O
HOH
1_555
77.8
A
MBD
301
A
D
OA1
MBD
1_555
A
FE2
500
B
FE
FE2
1_555
A
HOH
3001
B
G
O
HOH
1_555
30.7
A
MBD
301
A
D
OA2
MBD
1_555
A
FE2
500
B
FE
FE2
1_555
A
HOH
3001
B
G
O
HOH
1_555
93.4
A
HIS
146
A
NE2
HIS
145
1_555
A
FE2
500
B
FE
FE2
1_555
A
HOH
3012
B
G
O
HOH
1_555
95.7
A
HIS
210
A
NE2
HIS
209
1_555
A
FE2
500
B
FE
FE2
1_555
A
HOH
3012
B
G
O
HOH
1_555
109.4
A
GLU
260
A
OE2
GLU
259
1_555
A
FE2
500
B
FE
FE2
1_555
A
HOH
3012
B
G
O
HOH
1_555
146.2
A
MBD
301
A
D
OA1
MBD
1_555
A
FE2
500
B
FE
FE2
1_555
A
HOH
3012
B
G
O
HOH
1_555
47.3
A
MBD
301
A
D
OA2
MBD
1_555
A
FE2
500
B
FE
FE2
1_555
A
HOH
3012
B
G
O
HOH
1_555
58.0
A
HOH
3001
B
G
O
HOH
1_555
A
FE2
500
B
FE
FE2
1_555
A
HOH
3012
B
G
O
HOH
1_555
76.0
A
HIS
146
A
NE2
HIS
145
1_555
A
FE2
500
B
FE
FE2
1_555
A
HOH
9001
A
G
O
HOH
1_555
79.8
A
HIS
210
A
NE2
HIS
209
1_555
A
FE2
500
B
FE
FE2
1_555
A
HOH
9001
A
G
O
HOH
1_555
83.1
A
GLU
260
A
OE2
GLU
259
1_555
A
FE2
500
B
FE
FE2
1_555
A
HOH
9001
A
G
O
HOH
1_555
172.2
A
MBD
301
A
D
OA1
MBD
1_555
A
FE2
500
B
FE
FE2
1_555
A
HOH
9001
A
G
O
HOH
1_555
81.3
A
MBD
301
A
D
OA2
MBD
1_555
A
FE2
500
B
FE
FE2
1_555
A
HOH
9001
A
G
O
HOH
1_555
71.0
A
HOH
3001
B
G
O
HOH
1_555
A
FE2
500
B
FE
FE2
1_555
A
HOH
9001
A
G
O
HOH
1_555
107.2
A
HOH
3012
B
G
O
HOH
1_555
A
FE2
500
B
FE
FE2
1_555
A
HOH
9001
A
G
O
HOH
1_555
34.6
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
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
2_555
-x,-y,z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
3_555
-y,x,z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
4_555
y,-x,z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
5_556
-x,y,-z+1
crystal symmetry operation
0.0000000000
0.0000000000
110.6000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
6_556
x,-y,-z+1
crystal symmetry operation
0.0000000000
0.0000000000
110.6000000000
0.0000000000
1.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
7_556
y,x,-z+1
crystal symmetry operation
0.0000000000
0.0000000000
110.6000000000
0.0000000000
-1.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
8_556
-y,-x,-z+1
crystal symmetry operation
0.0000000000
0.0000000000
110.6000000000
A
N
MET
30
A
N
MET
29
A
O
ARG
42
A
O
ARG
41
A
N
PHE
41
A
N
PHE
40
A
O
ILE
50
A
O
ILE
49
A
O
GLN
53
A
O
GLN
52
A
N
PHE
11
A
N
PHE
10
A
N
GLY
10
A
N
GLY
9
A
O
ALA
61
A
O
ALA
60
A
N
TYR
65
A
N
TYR
64
A
O
GLU
115
A
O
GLU
114
A
O
LEU
114
A
O
LEU
113
A
N
PHE
106
A
N
PHE
105
A
O
THR
105
A
O
THR
104
A
N
THR
88
A
N
THR
87
A
O
HIS
277
A
O
HIS
276
A
N
VAL
172
A
N
VAL
171
A
N
GLN
168
A
N
GLN
167
A
O
HIS
189
A
O
HIS
188
A
N
LEU
188
A
N
LEU
187
A
O
LEU
197
A
O
LEU
196
A
O
ALA
198
A
O
ALA
197
A
N
ARG
149
A
N
ARG
148
A
N
HIS
146
A
N
HIS
145
A
O
MET
212
A
O
MET
211
A
N
PHE
211
A
N
PHE
210
A
O
GLU
260
A
O
GLU
259
A
O
TRP
263
A
O
TRP
262
A
N
VAL
247
A
N
VAL
246
A
O
SER
248
A
O
SER
247
A
N
GLY
239
A
N
GLY
238
A
N
ARG
240
A
N
ARG
239
A
O
MET
282
A
O
MET
281
1
A
ASP
290
A
ASP
289
1
Y
1
A
LYS
291
A
LYS
290
1
Y
1
A
ALA
292
A
ALA
291
1
Y
1
A
ALA
293
A
ALA
292
1
Y
1
A
ALA
294
A
ALA
293
1
Y
1
A
ARG
295
A
ARG
294
1
Y
1
A
ASN
296
A
ASN
295
1
Y
1
A
LYS
297
A
LYS
296
1
Y
1
A
ALA
298
A
ALA
297
1
Y
1
A
ASP
44
-157.25
-153.14
1
A
PHE
106
-170.91
-172.98
1
A
ALA
133
-69.41
96.94
1
A
THR
139
-130.51
-100.05
1
A
MET
177
-110.44
78.73
1
A
ASN
191
-163.71
-161.56
24.3
ALL FE-PROTEIN BOND DISTANCES WERE HARMONICALLY RESTRAINED TO AN EQUILIBRIUM DISTANCE OF 2.2 ANGSTROMS USING A WEAK FORCE CONSTANT OF 10 KCAL/(MOLE X ANGSTROM-SQUARED). BOND LENGTH, BOND ANGLE, AND PLANARITY RESTRAINTS SIMILAR TO THOSE USED FOR AROMATIC SIDE CHAINS WERE APPLIED TO HET GROUP CAQ (CATECHOL). FE-CAQ AND FE-WATER BOND DISTANCES WERE NOT RESTRAINED.
THE REFINED MODEL INCLUDES TWO MUTALLY EXCLUSIVE STRUCTURES IN THE VICINITY OF THE ACTIVE SITE. STRUCTURE ONE (labeled with alternate conformation marker A) INCLUDES A SUBSTRATE 3-METHYL-CATECHOL (MBD 301) AND WATERS 9001 and 9002 AT 50% OCCUPANCY. ATOMS OA1 AND OA2 OF MBD 301 AND WATER 9001 ARE COORDINATED TO FE2 500. STRUCTURE TWO (labeled with alternate conformation marker B) INCLUDES ONE MOLECULE OF T-BUTANOL (TBU 600) AND WATERS 3001, 3012, AND 4014 AT 50% OCCUPANCY, AND IS EQUIVALENT TO THE SUBSTRATE-FREE STRUCTURE WHERE WATERS 3001 AND 3012 ARE COORDINATED TO FE2 500.
0.1950000
0.1680000
0.2070000
0.1990000
1.9
7.0
1811
30504
30504
97.0
RANDOM
1
THROUGHOUT
0
0
MOLECULAR REPLACEMENT
1HAN
Engh & Huber
1.9
7.0
121
2358
21
0
2216
0.01
1.47
1.9
1.0
1.5
2.8
1.0
1.5
0.2980000
0.2730000
1.93
46
767
81.9
1.9
40
1KNF
32641
32641
0
0
0.0800000
1
44.8
6.9
97.0
1.9
1.97
5.1
2397
0.2700000
1
3.8
73.1
phasing
AMoRE
refinement
X-PLOR
3.1
data reduction
DENZO
data scaling
SCALEPACK
Crystal Structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase Complexed with 3-methyl Catechol under Anaerobic Condition
1
N
N
2
N
N
2
N
N
3
N
N
4
N
N
4
N
N
5
N
N
The biological assembly is homo-octamer generated by crystallographic symmetry
A
ASP
15
A
ASP
14
HELX_P
A
LYS
26
A
LYS
25
1
1
12
A
ASP
69
A
ASP
68
HELX_P
A
ALA
83
A
ALA
82
1
2
15
A
ASP
91
A
ASP
90
HELX_P
A
GLY
99
A
GLY
98
1
3
9
A
THR
139
A
THR
138
HELX_P
A
GLY
143
A
GLY
142
5
4
5
A
ASP
153
A
ASP
152
HELX_P
A
VAL
164
A
VAL
163
1
5
12
A
SER
217
A
SER
216
HELX_P
A
ALA
230
A
ALA
229
1
6
14
metalc
2.158
A
HIS
146
A
NE2
HIS
145
1_555
A
FE2
500
B
FE
FE2
1_555
metalc
2.577
A
HIS
189
A
NE2
HIS
188
1_555
A
FE2
501
C
FE
FE2
1_555
metalc
2.284
A
HIS
210
A
NE2
HIS
209
1_555
A
FE2
500
B
FE
FE2
1_555
metalc
1.965
A
GLU
260
A
OE2
GLU
259
1_555
A
FE2
500
B
FE
FE2
1_555
metalc
2.327
A
A
MBD
301
D
OA1
MBD
1_555
A
FE2
500
B
FE
FE2
1_555
metalc
2.430
A
A
MBD
301
D
OA2
MBD
1_555
A
FE2
500
B
FE
FE2
1_555
metalc
2.650
B
A
FE2
500
B
FE
FE2
1_555
A
HOH
3001
G
O
HOH
1_555
metalc
1.905
B
A
FE2
500
B
FE
FE2
1_555
A
HOH
3012
G
O
HOH
1_555
metalc
2.309
A
A
FE2
500
B
FE
FE2
1_555
A
HOH
9001
G
O
HOH
1_555
OXIDOREDUCTASE
dioxygenase, 2, 3-dihydroxybiphenyl, 3-methyl catechol, oxidoreductase
BPHC_BURCE
UNP
1
1
P47228
SIRSLGYMGFAVSDVAAWRSFLTQKLGLMEAGTTDNGDLFRIDSRAWRIAVQQGEVDDLAFAGYEVADAAGLAQMADKLK
QAGIAVTTGDASLARRRGVTGLITFADPFGLPLEIYYGASEVFEKPFLPGAAVSGFLTGEQGLGHFVRCVPDSDKALAFY
TDVLGFQLSDVIDMKMGPDVTVPAYFLHCNERHHTLAIAAFPLPKRIHHFMLEVASLDDVGFAFDRVDADGLITSTLGRH
TNDHMVSFYASTPSGVEVEYGWSARTVDRSWVVVRHDSPSMWGHKSVRDKAAARNKA
1
297
1KNF
2
298
P47228
A
1
1
297
8
10
anti-parallel
anti-parallel
parallel
anti-parallel
parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
A
MET
30
A
MET
29
A
THR
35
A
THR
34
A
GLY
38
A
GLY
37
A
ARG
42
A
ARG
41
A
ILE
50
A
ILE
49
A
GLN
54
A
GLN
53
A
SER
5
A
SER
4
A
VAL
13
A
VAL
12
A
ASP
59
A
ASP
58
A
GLU
66
A
GLU
65
A
PRO
113
A
PRO
112
A
TYR
118
A
TYR
117
A
GLY
102
A
GLY
101
A
ALA
107
A
ALA
106
A
THR
88
A
THR
87
A
THR
89
A
THR
88
A
VAL
275
A
VAL
274
A
HIS
277
A
HIS
276
A
GLN
168
A
GLN
167
A
LYS
176
A
LYS
175
A
THR
182
A
THR
181
A
HIS
189
A
HIS
188
A
LEU
197
A
LEU
196
A
ALA
200
A
ALA
199
A
HIS
146
A
HIS
145
A
CYS
150
A
CYS
149
A
ILE
208
A
ILE
207
A
GLU
214
A
GLU
213
A
GLU
258
A
GLU
257
A
TRP
263
A
TRP
262
A
VAL
247
A
VAL
246
A
SER
252
A
SER
251
A
ILE
234
A
ILE
233
A
HIS
241
A
HIS
240
A
SER
281
A
SER
280
A
GLY
284
A
GLY
283
BINDING SITE FOR RESIDUE FE2 A 500
A
FE2
500
Software
7
BINDING SITE FOR RESIDUE FE2 A 501
A
FE2
501
Software
1
BINDING SITE FOR RESIDUE MBD A 301
A
MBD
301
Software
14
BINDING SITE FOR RESIDUE TBU A 601
A
TBU
601
Software
3
BINDING SITE FOR RESIDUE TBU A 600
A
TBU
600
Software
3
A
HIS
146
A
HIS
145
7
1_555
A
HIS
210
A
HIS
209
7
1_555
A
GLU
260
A
GLU
259
7
1_555
A
MBD
301
D
MBD
7
1_555
A
HOH
3001
G
HOH
7
1_555
A
HOH
3012
G
HOH
7
1_555
A
HOH
9001
G
HOH
7
1_555
A
HIS
189
A
HIS
188
1
1_555
A
HIS
146
A
HIS
145
14
1_555
A
PHE
187
A
PHE
186
14
1_555
A
HIS
195
A
HIS
194
14
1_555
A
HIS
210
A
HIS
209
14
1_555
A
HIS
241
A
HIS
240
14
1_555
A
ASN
243
A
ASN
242
14
1_555
A
ASP
244
A
ASP
243
14
1_555
A
TYR
250
A
TYR
249
14
1_555
A
GLU
260
A
GLU
259
14
1_555
A
FE2
500
B
FE2
14
1_555
A
HOH
3001
G
HOH
14
1_555
A
HOH
3012
G
HOH
14
1_555
A
HOH
9001
G
HOH
14
1_555
A
HOH
9002
G
HOH
14
1_555
A
SER
236
A
SER
235
3
1_555
A
ARG
289
A
ARG
288
3
1_555
A
TBU
600
F
TBU
3
1_555
A
TYR
250
A
TYR
249
3
1_555
A
PRO
280
A
PRO
279
3
1_555
A
TBU
601
E
TBU
3
1_555
97
I 4 2 2