0.020318
0.000000
0.000000
0.000000
0.013212
0.000000
0.000000
0.000000
0.025462
0.00000
0.00000
0.00000
Tanaka, Y.
Suenaga, A.
Tsumoto, K.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
49.217
75.686
39.274
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C34 H32 Fe N4 O4
616.487
PROTOPORPHYRIN IX CONTAINING FE
HEME
non-polymer
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
N
N
83
N
O
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
N
N
95
S
C
N
96
N
C
N
97
N
O
N
98
N
C
N
99
N
C
N
100
N
C
N
101
N
O
N
102
N
O
N
103
N
O
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
H
N
110
N
H
N
111
N
H
N
112
N
H
N
113
N
N
N
114
N
C
N
115
N
C
N
116
N
O
N
117
N
O
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
C
N
124
N
C
N
125
N
C
N
126
N
C
Y
127
N
C
Y
128
N
C
Y
129
N
C
Y
130
N
C
N
131
N
C
N
132
N
C
N
133
N
C
N
134
N
C
N
135
N
O
N
136
N
O
N
137
N
C
N
138
N
C
N
139
N
C
N
140
N
C
N
141
N
C
N
142
N
C
N
143
N
C
Y
144
N
C
Y
145
N
C
Y
146
N
C
Y
147
N
C
N
148
N
C
N
149
N
C
N
150
N
C
N
151
N
C
N
152
N
C
N
153
N
C
N
154
N
C
N
155
N
C
N
156
N
C
N
157
N
C
N
158
N
C
N
159
N
O
N
160
N
O
Y
161
N
N
N
162
N
N
Y
163
N
N
N
164
N
N
N
165
N
FE
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
H
N
170
N
H
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
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
H
N
197
N
H
N
198
N
N
N
199
S
C
N
200
N
C
N
201
N
O
N
202
N
C
Y
203
N
C
Y
204
N
N
Y
205
N
C
Y
206
N
C
Y
207
N
N
N
208
N
O
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
H
N
217
N
H
N
218
N
H
N
219
N
O
N
220
N
H
N
221
N
H
N
222
N
N
N
223
S
C
N
224
N
C
N
225
N
O
N
226
S
C
N
227
N
C
N
228
N
C
N
229
N
C
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
H
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
N
N
245
S
C
N
246
N
C
N
247
N
O
N
248
N
C
N
249
N
C
N
250
N
C
N
251
N
C
N
252
N
O
N
253
N
H
N
254
N
H
N
255
N
H
N
256
N
H
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
N
N
267
S
C
N
268
N
C
N
269
N
O
N
270
N
C
N
271
N
C
N
272
N
C
N
273
N
C
N
274
N
N
N
275
N
O
N
276
N
H
N
277
N
H
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
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
S
N
298
N
C
N
299
N
O
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
H
N
309
N
H
N
310
N
H
N
311
N
N
N
312
S
C
N
313
N
C
N
314
N
O
N
315
N
C
Y
316
N
C
Y
317
N
C
Y
318
N
C
Y
319
N
C
Y
320
N
C
Y
321
N
C
N
322
N
O
N
323
N
H
N
324
N
H
N
325
N
H
N
326
N
H
N
327
N
H
N
328
N
H
N
329
N
H
N
330
N
H
N
331
N
H
N
332
N
H
N
333
N
H
N
334
N
N
N
335
S
C
N
336
N
C
N
337
N
O
N
338
N
C
N
339
N
C
N
340
N
C
N
341
N
O
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
N
N
352
S
C
N
353
N
C
N
354
N
O
N
355
N
C
N
356
N
O
N
357
N
O
N
358
N
H
N
359
N
H
N
360
N
H
N
361
N
H
N
362
N
H
N
363
N
H
N
364
N
H
N
365
N
N
N
366
S
C
N
367
N
C
N
368
N
O
N
369
R
C
N
370
N
O
N
371
N
C
N
372
N
O
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
N
N
383
S
C
N
384
N
C
N
385
N
O
N
386
N
C
Y
387
N
C
Y
388
N
C
Y
389
N
C
Y
390
N
N
Y
391
N
C
Y
392
N
C
Y
393
N
C
Y
394
N
C
Y
395
N
C
N
396
N
O
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
H
N
406
N
H
N
407
N
H
N
408
N
H
N
409
N
N
N
410
S
C
N
411
N
C
N
412
N
O
N
413
N
C
Y
414
N
C
Y
415
N
C
Y
416
N
C
Y
417
N
C
Y
418
N
C
Y
419
N
C
N
420
N
O
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
H
N
432
N
H
N
433
N
N
N
434
S
C
N
435
N
C
N
436
N
O
N
437
N
C
N
438
N
C
N
439
N
C
N
440
N
O
N
441
N
H
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
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
doub
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
doub
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
doub
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
doub
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
doub
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
doub
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
doub
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
doub
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
doub
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
doub
N
118
N
sing
N
119
N
sing
N
120
N
doub
N
121
N
sing
N
122
N
sing
N
123
N
doub
N
124
N
sing
N
125
N
doub
N
126
N
sing
N
127
N
sing
Y
128
N
doub
Y
129
N
sing
Y
130
N
sing
N
131
N
sing
Y
132
N
doub
N
133
N
sing
Y
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
doub
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
doub
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
doub
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
doub
N
157
N
sing
N
158
N
sing
N
159
N
sing
Y
160
N
sing
Y
161
N
sing
Y
162
N
doub
N
163
N
sing
Y
164
N
sing
N
165
N
sing
Y
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
doub
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
doub
N
176
N
doub
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
doub
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
doub
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
Y
209
N
sing
Y
210
N
doub
Y
211
N
doub
N
212
N
sing
Y
213
N
sing
N
214
N
sing
Y
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
doub
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
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
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
doub
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
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
doub
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
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
doub
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
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
doub
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
Y
317
N
doub
Y
318
N
sing
Y
319
N
sing
N
320
N
sing
Y
321
N
doub
N
322
N
sing
Y
323
N
doub
N
324
N
sing
Y
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
doub
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
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
doub
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
sing
N
365
N
doub
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
sing
N
370
N
sing
N
371
N
sing
N
372
N
sing
N
373
N
sing
N
374
N
sing
N
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
doub
N
382
N
sing
N
383
N
sing
N
384
N
sing
N
385
N
sing
Y
386
N
doub
Y
387
N
sing
Y
388
N
sing
N
389
N
sing
Y
390
N
doub
Y
391
N
sing
Y
392
N
sing
N
393
N
sing
Y
394
N
sing
Y
395
N
doub
N
396
N
sing
Y
397
N
doub
N
398
N
sing
Y
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
N
407
N
sing
N
408
N
sing
N
409
N
doub
N
410
N
sing
N
411
N
sing
N
412
N
sing
N
413
N
sing
Y
414
N
doub
Y
415
N
sing
Y
416
N
sing
N
417
N
sing
Y
418
N
doub
N
419
N
sing
Y
420
N
doub
N
421
N
sing
Y
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
doub
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
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
283
28649
28659
10.1074/jbc.M803383200
18667422
Structural basis for multimeric heme complexation through a specific protein-heme interaction: the case of the third neat domain of IsdH from Staphylococcus aureus
2008
10.2210/pdb2z6f/pdb
pdb_00002z6f
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
1
CCD
2007-03-16
ADSC QUANTUM 210
SINGLE WAVELENGTH
M
x-ray
1
1.00000
1.0
AR-NW12A
Photon Factory
1.00000
SYNCHROTRON
PHOTON FACTORY BEAMLINE AR-NW12A
14854.489
Iron-regulated surface determinant protein H
NEAT 3 domain, residue 539-664
1
man
polymer
616.487
PROTOPORPHYRIN IX CONTAINING FE
1
syn
non-polymer
18.015
water
88
nat
water
Haptoglobin receptor A, Staphylococcus aureus surface protein I
no
no
GSAMAPTNDQLTDLQEAHFVVFESEENSESVMDGFVEHPFYTATLNGQKYVVMKTKDDSYWKDLIVEGKRVTTVSKDPKN
NSRTLIFPYIPDKAVYNAIVKVVVANIGYEGQYHVRIINQDINTKDDDTSQ
GSAMAPTNDQLTDLQEAHFVVFESEENSESVMDGFVEHPFYTATLNGQKYVVMKTKDDSYWKDLIVEGKRVTTVSKDPKN
NSRTLIFPYIPDKAVYNAIVKVVVANIGYEGQYHVRIINQDINTKDDDTSQ
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
Mu50
sample
isdH
158878
Staphylococcus aureus
469008
Escherichia coli
BL21(DE3)
plasmid
pDBHT3
1
2.46
50.04
VAPOR DIFFUSION, SITTING DROP
10.5
100mM CAPS, 20% polyethylene glycol 8000, 200mM NaCl, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
293
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_ref_seq_dif
repository
Initial release
Version format compliance
Data collection
Database references
Refinement description
1
0
2008-07-29
1
1
2011-07-13
1
2
2023-11-01
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
Crystal structure of the protein in apo form
Crystal structure of the protein which has a similar motif
Crystal structure of the protein which has a similar motif
Crystal structure of the protein which has a similar motif
Solution structure of the protein which has a similar motif
Crystal structure of the protein which has a similar motif
PDBJ
Y
PDBJ
2007-07-31
REL
REL
HEM
PROTOPORPHYRIN IX CONTAINING FE
HOH
water
2E7D
PDB ENTRY 2E7D
PDB
experimental model
HEM
3747
2
HEM
HEM
3747
A
HOH
1
3
HOH
HOH
1
A
HOH
2
3
HOH
HOH
2
A
HOH
3
3
HOH
HOH
3
A
HOH
4
3
HOH
HOH
4
A
HOH
5
3
HOH
HOH
5
A
HOH
6
3
HOH
HOH
6
A
HOH
7
3
HOH
HOH
7
A
HOH
8
3
HOH
HOH
8
A
HOH
9
3
HOH
HOH
9
A
HOH
10
3
HOH
HOH
10
A
HOH
11
3
HOH
HOH
11
A
HOH
12
3
HOH
HOH
12
A
HOH
13
3
HOH
HOH
13
A
HOH
14
3
HOH
HOH
14
A
HOH
15
3
HOH
HOH
15
A
HOH
16
3
HOH
HOH
16
A
HOH
17
3
HOH
HOH
17
A
HOH
18
3
HOH
HOH
18
A
HOH
19
3
HOH
HOH
19
A
HOH
20
3
HOH
HOH
20
A
HOH
23
3
HOH
HOH
23
A
HOH
24
3
HOH
HOH
24
A
HOH
25
3
HOH
HOH
25
A
HOH
26
3
HOH
HOH
26
A
HOH
27
3
HOH
HOH
27
A
HOH
29
3
HOH
HOH
29
A
HOH
30
3
HOH
HOH
30
A
HOH
31
3
HOH
HOH
31
A
HOH
33
3
HOH
HOH
33
A
HOH
34
3
HOH
HOH
34
A
HOH
35
3
HOH
HOH
35
A
HOH
36
3
HOH
HOH
36
A
HOH
37
3
HOH
HOH
37
A
HOH
38
3
HOH
HOH
38
A
HOH
39
3
HOH
HOH
39
A
HOH
40
3
HOH
HOH
40
A
HOH
41
3
HOH
HOH
41
A
HOH
42
3
HOH
HOH
42
A
HOH
44
3
HOH
HOH
44
A
HOH
45
3
HOH
HOH
45
A
HOH
46
3
HOH
HOH
46
A
HOH
47
3
HOH
HOH
47
A
HOH
49
3
HOH
HOH
49
A
HOH
50
3
HOH
HOH
50
A
HOH
51
3
HOH
HOH
51
A
HOH
52
3
HOH
HOH
52
A
HOH
53
3
HOH
HOH
53
A
HOH
56
3
HOH
HOH
56
A
HOH
58
3
HOH
HOH
58
A
HOH
59
3
HOH
HOH
59
A
HOH
60
3
HOH
HOH
60
A
HOH
61
3
HOH
HOH
61
A
HOH
62
3
HOH
HOH
62
A
HOH
63
3
HOH
HOH
63
A
HOH
64
3
HOH
HOH
64
A
HOH
65
3
HOH
HOH
65
A
HOH
66
3
HOH
HOH
66
A
HOH
67
3
HOH
HOH
67
A
HOH
68
3
HOH
HOH
68
A
HOH
69
3
HOH
HOH
69
A
HOH
71
3
HOH
HOH
71
A
HOH
72
3
HOH
HOH
72
A
HOH
75
3
HOH
HOH
75
A
HOH
76
3
HOH
HOH
76
A
HOH
78
3
HOH
HOH
78
A
HOH
79
3
HOH
HOH
79
A
HOH
80
3
HOH
HOH
80
A
HOH
82
3
HOH
HOH
82
A
HOH
83
3
HOH
HOH
83
A
HOH
85
3
HOH
HOH
85
A
HOH
86
3
HOH
HOH
86
A
HOH
87
3
HOH
HOH
87
A
HOH
89
3
HOH
HOH
89
A
HOH
90
3
HOH
HOH
90
A
HOH
92
3
HOH
HOH
92
A
HOH
93
3
HOH
HOH
93
A
HOH
94
3
HOH
HOH
94
A
HOH
95
3
HOH
HOH
95
A
HOH
96
3
HOH
HOH
96
A
HOH
98
3
HOH
HOH
98
A
HOH
100
3
HOH
HOH
100
A
HOH
102
3
HOH
HOH
102
A
HOH
103
3
HOH
HOH
103
A
HOH
104
3
HOH
HOH
104
A
HOH
105
3
HOH
HOH
105
A
HOH
106
3
HOH
HOH
106
A
HOH
107
3
HOH
HOH
107
A
HOH
108
3
HOH
HOH
108
A
n
1
534
A
n
2
535
A
n
3
536
A
n
4
537
A
n
5
538
A
n
6
539
A
n
7
540
A
n
8
541
A
n
9
542
A
n
10
543
A
LEU
544
n
11
LEU
544
A
THR
545
n
12
THR
545
A
ASP
546
n
13
ASP
546
A
LEU
547
n
14
LEU
547
A
GLN
548
n
15
GLN
548
A
GLU
549
n
16
GLU
549
A
ALA
550
n
17
ALA
550
A
HIS
551
n
18
HIS
551
A
PHE
552
n
19
PHE
552
A
VAL
553
n
20
VAL
553
A
VAL
554
n
21
VAL
554
A
PHE
555
n
22
PHE
555
A
GLU
556
n
23
GLU
556
A
SER
557
n
24
SER
557
A
GLU
558
n
25
GLU
558
A
GLU
559
n
26
GLU
559
A
ASN
560
n
27
ASN
560
A
SER
561
n
28
SER
561
A
GLU
562
n
29
GLU
562
A
SER
563
n
30
SER
563
A
VAL
564
n
31
VAL
564
A
MET
565
n
32
MET
565
A
ASP
566
n
33
ASP
566
A
GLY
567
n
34
GLY
567
A
PHE
568
n
35
PHE
568
A
VAL
569
n
36
VAL
569
A
GLU
570
n
37
GLU
570
A
HIS
571
n
38
HIS
571
A
PRO
572
n
39
PRO
572
A
PHE
573
n
40
PHE
573
A
TYR
574
n
41
TYR
574
A
THR
575
n
42
THR
575
A
ALA
576
n
43
ALA
576
A
THR
577
n
44
THR
577
A
LEU
578
n
45
LEU
578
A
ASN
579
n
46
ASN
579
A
GLY
580
n
47
GLY
580
A
GLN
581
n
48
GLN
581
A
LYS
582
n
49
LYS
582
A
TYR
583
n
50
TYR
583
A
VAL
584
n
51
VAL
584
A
VAL
585
n
52
VAL
585
A
MET
586
n
53
MET
586
A
LYS
587
n
54
LYS
587
A
THR
588
n
55
THR
588
A
LYS
589
n
56
LYS
589
A
ASP
590
n
57
ASP
590
A
ASP
591
n
58
ASP
591
A
SER
592
n
59
SER
592
A
TYR
593
n
60
TYR
593
A
TRP
594
n
61
TRP
594
A
LYS
595
n
62
LYS
595
A
ASP
596
n
63
ASP
596
A
LEU
597
n
64
LEU
597
A
ILE
598
n
65
ILE
598
A
VAL
599
n
66
VAL
599
A
GLU
600
n
67
GLU
600
A
GLY
601
n
68
GLY
601
A
LYS
602
n
69
LYS
602
A
ARG
603
n
70
ARG
603
A
VAL
604
n
71
VAL
604
A
THR
605
n
72
THR
605
A
THR
606
n
73
THR
606
A
VAL
607
n
74
VAL
607
A
SER
608
n
75
SER
608
A
LYS
609
n
76
LYS
609
A
ASP
610
n
77
ASP
610
A
PRO
611
n
78
PRO
611
A
LYS
612
n
79
LYS
612
A
ASN
613
n
80
ASN
613
A
ASN
614
n
81
ASN
614
A
SER
615
n
82
SER
615
A
ARG
616
n
83
ARG
616
A
THR
617
n
84
THR
617
A
LEU
618
n
85
LEU
618
A
ILE
619
n
86
ILE
619
A
PHE
620
n
87
PHE
620
A
PRO
621
n
88
PRO
621
A
TYR
622
n
89
TYR
622
A
ILE
623
n
90
ILE
623
A
PRO
624
n
91
PRO
624
A
ASP
625
n
92
ASP
625
A
LYS
626
n
93
LYS
626
A
ALA
627
n
94
ALA
627
A
VAL
628
n
95
VAL
628
A
TYR
629
n
96
TYR
629
A
ASN
630
n
97
ASN
630
A
ALA
631
n
98
ALA
631
A
ILE
632
n
99
ILE
632
A
VAL
633
n
100
VAL
633
A
LYS
634
n
101
LYS
634
A
VAL
635
n
102
VAL
635
A
VAL
636
n
103
VAL
636
A
VAL
637
n
104
VAL
637
A
ALA
638
n
105
ALA
638
A
ASN
639
n
106
ASN
639
A
ILE
640
n
107
ILE
640
A
GLY
641
n
108
GLY
641
A
TYR
642
n
109
TYR
642
A
GLU
643
n
110
GLU
643
A
GLY
644
n
111
GLY
644
A
GLN
645
n
112
GLN
645
A
TYR
646
n
113
TYR
646
A
HIS
647
n
114
HIS
647
A
VAL
648
n
115
VAL
648
A
ARG
649
n
116
ARG
649
A
ILE
650
n
117
ILE
650
A
ILE
651
n
118
ILE
651
A
ASN
652
n
119
ASN
652
A
GLN
653
n
120
GLN
653
A
ASP
654
n
121
ASP
654
A
ILE
655
n
122
ILE
655
A
n
123
656
A
n
124
657
A
n
125
658
A
n
126
659
A
n
127
660
A
n
128
661
A
n
129
662
A
n
130
663
A
n
131
664
A
software_defined_assembly
PISA
2
dimeric
2970
-45
12060
A
TYR
642
A
OH
TYR
109
1_555
A
HEM
3747
B
FE
HEM
1_555
A
HEM
3747
B
NA
HEM
1_555
93.8
A
TYR
642
A
OH
TYR
109
1_555
A
HEM
3747
B
FE
HEM
1_555
A
HEM
3747
B
NB
HEM
1_555
95.6
A
HEM
3747
B
NA
HEM
1_555
A
HEM
3747
B
FE
HEM
1_555
A
HEM
3747
B
NB
HEM
1_555
91.4
A
TYR
642
A
OH
TYR
109
1_555
A
HEM
3747
B
FE
HEM
1_555
A
HEM
3747
B
NC
HEM
1_555
100.1
A
HEM
3747
B
NA
HEM
1_555
A
HEM
3747
B
FE
HEM
1_555
A
HEM
3747
B
NC
HEM
1_555
166.1
A
HEM
3747
B
NB
HEM
1_555
A
HEM
3747
B
FE
HEM
1_555
A
HEM
3747
B
NC
HEM
1_555
87.2
A
TYR
642
A
OH
TYR
109
1_555
A
HEM
3747
B
FE
HEM
1_555
A
HEM
3747
B
ND
HEM
1_555
99.3
A
HEM
3747
B
NA
HEM
1_555
A
HEM
3747
B
FE
HEM
1_555
A
HEM
3747
B
ND
HEM
1_555
83.3
A
HEM
3747
B
NB
HEM
1_555
A
HEM
3747
B
FE
HEM
1_555
A
HEM
3747
B
ND
HEM
1_555
164.4
A
HEM
3747
B
NC
HEM
1_555
A
HEM
3747
B
FE
HEM
1_555
A
HEM
3747
B
ND
HEM
1_555
94.4
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
A
N
THR
545
A
N
THR
12
A
O
THR
577
A
O
THR
44
A
N
TYR
574
A
N
TYR
41
A
O
VAL
585
A
O
VAL
52
A
N
VAL
584
A
N
VAL
51
A
O
PHE
620
A
O
PHE
87
A
O
SER
615
A
O
SER
82
A
N
ASP
610
A
N
ASP
77
A
N
PHE
555
A
N
PHE
22
A
O
ARG
649
A
O
ARG
116
A
O
ILE
650
A
O
ILE
117
A
N
TYR
629
A
N
TYR
96
A
O
LYS
634
A
O
LYS
101
A
N
LYS
595
A
N
LYS
62
A
N
VAL
599
A
N
VAL
66
A
O
LYS
602
A
O
LYS
69
1
A
GLY
534
A
GLY
1
1
Y
1
A
SER
535
A
SER
2
1
Y
1
A
ALA
536
A
ALA
3
1
Y
1
A
MET
537
A
MET
4
1
Y
1
A
ALA
538
A
ALA
5
1
Y
1
A
PRO
539
A
PRO
6
1
Y
1
A
THR
540
A
THR
7
1
Y
1
A
ASN
541
A
ASN
8
1
Y
1
A
ASP
542
A
ASP
9
1
Y
1
A
GLN
543
A
GLN
10
1
Y
1
A
ASN
656
A
ASN
123
1
Y
1
A
THR
657
A
THR
124
1
Y
1
A
LYS
658
A
LYS
125
1
Y
1
A
ASP
659
A
ASP
126
1
Y
1
A
ASP
660
A
ASP
127
1
Y
1
A
ASP
661
A
ASP
128
1
Y
1
A
THR
662
A
THR
129
1
Y
1
A
SER
663
A
SER
130
1
Y
1
A
GLN
664
A
GLN
131
1
Y
1
A
A
OD2
O
ASP
HOH
596
52
1.85
1
A
A
OE1
O
GLU
HOH
562
51
2.19
1
A
ASN
614
38.27
56.37
20.495
0.00
0.00
0.00
0.00
0.00
0.00
0.945
0.920
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.24175
0.19279
0.19747
1.90
17.62
1168
10756
9.8
98.46
2.959
0.089
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.151
0.148
0.80
0.80
1.20
PDB ENTRY 2E7D
MAXIMUM LIKELIHOOD
MASK
1.90
17.62
88
1039
43
0
908
0.016
0.022
978
1.750
2.077
1342
6.482
5.000
111
37.959
25.217
46
15.924
15.000
160
26.220
15.000
3
0.114
0.200
142
0.007
0.020
746
0.209
0.200
409
0.308
0.200
658
0.186
0.200
88
0.204
0.200
31
0.121
0.200
7
1.198
1.500
572
1.694
2.000
915
2.847
3.000
465
4.530
4.500
425
0.303
0.231
1.947
87
682
20
89.00
1.9
50
2Z6F
11976
0.069
1
6.8
98.6
1.90
1.97
0.285
5.9
90.5
refinement
REFMAC
5.2.0019
data collection
HKL-2000
data reduction
HKL-2000
data scaling
HKL-2000
phasing
MOLREP
Crystal structure of NEAT domain from Staphylococcus aureus in complex with heme
1
N
N
2
N
N
3
N
N
THE BIOLOGICAL MOLECULE FOR THE PROTEIN IS UNKNOWN. Although the asymmetrically related two molecules seems to be a stable dimer, the structure is one of the domain among three.
A
SER
563
A
SER
30
HELX_P
A
PHE
568
A
PHE
35
1
1
6
A
ASP
590
A
ASP
57
HELX_P
A
SER
592
A
SER
59
5
2
3
A
PRO
611
A
PRO
78
HELX_P
A
ASN
614
A
ASN
81
5
3
4
A
ALA
638
A
ALA
105
HELX_P
A
GLY
641
A
GLY
108
5
4
4
metalc
2.209
A
TYR
642
A
OH
TYR
109
1_555
A
HEM
3747
B
FE
HEM
1_555
HEME BINDING PROTEIN
IgG-like fold, Cell wall, Peptidoglycan-anchor, Secreted, HEME BINDING PROTEIN
A
HIS
571
A
HIS
38
1
A
PRO
572
A
PRO
39
-0.41
ISDH_STAAM
UNP
1
539
Q931P4
PTNDQLTDLQEAHFVVFESEENSESVMDGFVEHPFYTATLNGQKYVVMKTKDDSYWKDLIVEGKRVTTVSKDPKNNSRTL
IFPYIPDKAVYNAIVKVVVANIGYEGQYHVRIINQDINTKDDDTSQ
539
664
2Z6F
539
664
Q931P4
A
1
6
131
1
expression tag
GLY
534
2Z6F
A
Q931P4
UNP
1
1
expression tag
SER
535
2Z6F
A
Q931P4
UNP
2
1
expression tag
ALA
536
2Z6F
A
Q931P4
UNP
3
1
expression tag
MET
537
2Z6F
A
Q931P4
UNP
4
1
expression tag
ALA
538
2Z6F
A
Q931P4
UNP
5
5
5
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
THR
545
A
THR
12
A
ALA
550
A
ALA
17
A
PHE
573
A
PHE
40
A
LEU
578
A
LEU
45
A
GLN
581
A
GLN
48
A
LYS
587
A
LYS
54
A
SER
615
A
SER
82
A
PRO
621
A
PRO
88
A
THR
605
A
THR
72
A
ASP
610
A
ASP
77
A
PHE
552
A
PHE
19
A
GLU
556
A
GLU
23
A
TYR
642
A
TYR
109
A
ASN
652
A
ASN
119
A
VAL
628
A
VAL
95
A
VAL
637
A
VAL
104
A
TRP
594
A
TRP
61
A
VAL
599
A
VAL
66
A
LYS
602
A
LYS
69
A
ARG
603
A
ARG
70
BINDING SITE FOR RESIDUE HEM A3747
Software
12
A
HOH
2
C
HOH
12
1_555
A
HOH
33
C
HOH
12
1_555
A
HOH
76
C
HOH
12
1_555
A
SER
563
A
SER
30
12
1_555
A
VAL
564
A
VAL
31
12
2_555
A
PHE
568
A
PHE
35
12
1_555
A
TRP
594
A
TRP
61
12
1_555
A
VAL
635
A
VAL
102
12
1_555
A
ILE
640
A
ILE
107
12
1_555
A
TYR
642
A
TYR
109
12
1_555
A
TYR
646
A
TYR
113
12
1_555
A
VAL
648
A
VAL
115
12
1_555
18
P 21 21 2