.006867
.000000
.000000
.000000
.006867
.000000
.000000
.000000
.006867
.00000
.00000
.00000
Richard, S.B.
Ferrer, J.L.
Bowman, M.E.
Lillo, A.M.
Tetzlaff, C.N.
Cane, D.E.
Noel, J.P.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
24
90.00
90.00
90.00
145.630
145.630
145.630
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
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
Mn 2
54.938
MANGANESE (II) ION
non-polymer
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
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
N
N
89
S
C
N
90
N
C
N
91
N
O
N
92
N
C
N
93
N
C
N
94
N
C
N
95
N
O
N
96
N
N
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
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
N
N
109
S
C
N
110
N
C
N
111
N
O
N
112
N
C
N
113
N
C
N
114
N
C
N
115
N
O
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
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
N
N
128
N
C
N
129
N
C
N
130
N
O
N
131
N
O
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
N
N
138
S
C
N
139
N
C
N
140
N
O
N
141
N
C
Y
142
N
C
Y
143
N
N
Y
144
N
C
Y
145
N
C
Y
146
N
N
N
147
N
O
N
148
N
H
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
O
N
159
N
H
N
160
N
H
N
161
N
N
N
162
S
C
N
163
N
C
N
164
N
O
N
165
S
C
N
166
N
C
N
167
N
C
N
168
N
C
N
169
N
O
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
N
N
184
S
C
N
185
N
C
N
186
N
O
N
187
N
C
N
188
N
C
N
189
N
C
N
190
N
C
N
191
N
O
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
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
N
N
206
S
C
N
207
N
C
N
208
N
O
N
209
N
C
N
210
N
C
N
211
N
C
N
212
N
C
N
213
N
N
N
214
N
O
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
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
N
N
231
S
C
N
232
N
C
N
233
N
O
N
234
N
C
N
235
N
C
N
236
N
S
N
237
N
C
N
238
N
O
N
239
N
H
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
H
N
249
N
H
N
250
N
MN
N
251
N
N
N
252
S
C
N
253
N
C
N
254
N
O
N
255
N
C
Y
256
N
C
Y
257
N
C
Y
258
N
C
Y
259
N
C
Y
260
N
C
Y
261
N
C
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
H
N
271
N
H
N
272
N
H
N
273
N
H
N
274
N
N
N
275
S
C
N
276
N
C
N
277
N
O
N
278
N
C
N
279
N
C
N
280
N
C
N
281
N
O
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
O
N
297
N
O
N
298
N
H
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
N
N
306
S
C
N
307
N
C
N
308
N
O
N
309
R
C
N
310
N
O
N
311
N
C
N
312
N
O
N
313
N
H
N
314
N
H
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
N
N
323
S
C
N
324
N
C
N
325
N
O
N
326
N
C
Y
327
N
C
Y
328
N
C
Y
329
N
C
Y
330
N
N
Y
331
N
C
Y
332
N
C
Y
333
N
C
Y
334
N
C
Y
335
N
C
N
336
N
O
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
H
N
349
N
N
N
350
S
C
N
351
N
C
N
352
N
O
N
353
N
C
Y
354
N
C
Y
355
N
C
Y
356
N
C
Y
357
N
C
Y
358
N
C
Y
359
N
C
N
360
N
O
N
361
N
O
N
362
N
H
N
363
N
H
N
364
N
H
N
365
N
H
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
H
N
373
N
N
N
374
S
C
N
375
N
C
N
376
N
O
N
377
N
C
N
378
N
C
N
379
N
C
N
380
N
O
N
381
N
H
N
382
N
H
N
383
N
H
N
384
N
H
N
385
N
H
N
386
N
H
N
387
N
H
N
388
N
H
N
389
N
H
N
390
N
H
N
391
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
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
doub
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
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
doub
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
Y
248
N
doub
Y
249
N
sing
Y
250
N
sing
N
251
N
sing
Y
252
N
doub
N
253
N
sing
Y
254
N
doub
N
255
N
sing
Y
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
doub
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
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
doub
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
Y
322
N
sing
Y
323
N
sing
N
324
N
sing
Y
325
N
sing
Y
326
N
doub
N
327
N
sing
Y
328
N
doub
N
329
N
sing
Y
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
doub
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
Y
345
N
doub
Y
346
N
sing
Y
347
N
sing
N
348
N
sing
Y
349
N
doub
N
350
N
sing
Y
351
N
doub
N
352
N
sing
Y
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
sing
N
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
doub
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
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
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
277
8667
8672
10.1074/jbc.C100739200
11786530
Structure and mechanism of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase. An enzyme in the mevalonate-independent isoprenoid biosynthetic pathway.
2002
US
Nat.Struct.Biol.
NSBIEW
2024
1072-8368
8
641
648
10.1038/89691
Structure of 4-diphosphocytidyl-2-C-methylerythritol Synthetase Involved in Mevalonate-Independent Isoprenoid
Biosynthesis
2001
10.2210/pdb1knk/pdb
pdb_00001knk
1.000000
.000000
.000000
.000000
1.000000
.000000
.000000
.000000
1.000000
.00000
.00000
.00000
100
1
CCD
2001-10-10
ADSC QUANTUM 4
Si(111) OR Si(311) CRYSTALS, LN2 COOLED
SINGLE WAVELENGTH
M
x-ray
1
0.9793
1.0
ID14-4
ESRF
0.9793
SYNCHROTRON
ESRF BEAMLINE ID14-4
16920.531
2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
1
man
polymer
54.938
MANGANESE (II) ION
1
syn
non-polymer
18.015
water
11
nat
water
MECPS
no
no
MRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREA
WRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLIKATK
MRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREA
WRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLIKATK
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
Escherichia
Escherichia
Escherichia coli
sample
ispF
562
Escherichia coli
469008
Escherichia coli BL21(DE3)
BL21(DE3)
PLASMID
PHIS8
1
VAPOR DIFFUSION, HANGING DROP
6.5
(NH4)2SO4, PEG 400, NaI, PIPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
294
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
Version format compliance
Atomic model
Data collection
Database references
Derived calculations
Refinement description
1
0
2002-06-18
1
1
2008-04-27
1
2
2011-07-13
1
3
2011-11-16
1
4
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.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
Co-Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (ispF)
from E. coli involved in mevalonate-independent isoprenoid biosynthesis, complexed with
CMP/MECDP/Mn2+
RCSB
Y
RCSB
2001-12-18
REL
REL
MN
MANGANESE (II) ION
HOH
water
1KNJ
PDB ENTRY 1KNJ
PDB
experimental model
MN
1
2
MN
MN
201
A
HOH
1
3
HOH
HOH
202
A
HOH
2
3
HOH
HOH
203
A
HOH
3
3
HOH
HOH
204
A
HOH
4
3
HOH
HOH
205
A
HOH
5
3
HOH
HOH
206
A
HOH
6
3
HOH
HOH
207
A
HOH
7
3
HOH
HOH
208
A
HOH
8
3
HOH
HOH
209
A
HOH
9
3
HOH
HOH
210
A
HOH
10
3
HOH
HOH
211
A
HOH
11
3
HOH
HOH
212
A
MET
1
n
1
MET
1
A
ARG
2
n
2
ARG
2
A
ILE
3
n
3
ILE
3
A
GLY
4
n
4
GLY
4
A
HIS
5
n
5
HIS
5
A
GLY
6
n
6
GLY
6
A
PHE
7
n
7
PHE
7
A
ASP
8
n
8
ASP
8
A
VAL
9
n
9
VAL
9
A
HIS
10
n
10
HIS
10
A
ALA
11
n
11
ALA
11
A
PHE
12
n
12
PHE
12
A
GLY
13
n
13
GLY
13
A
GLY
14
n
14
GLY
14
A
GLU
15
n
15
GLU
15
A
GLY
16
n
16
GLY
16
A
PRO
17
n
17
PRO
17
A
ILE
18
n
18
ILE
18
A
ILE
19
n
19
ILE
19
A
ILE
20
n
20
ILE
20
A
GLY
21
n
21
GLY
21
A
GLY
22
n
22
GLY
22
A
VAL
23
n
23
VAL
23
A
ARG
24
n
24
ARG
24
A
ILE
25
n
25
ILE
25
A
PRO
26
n
26
PRO
26
A
TYR
27
n
27
TYR
27
A
GLU
28
n
28
GLU
28
A
LYS
29
n
29
LYS
29
A
GLY
30
n
30
GLY
30
A
LEU
31
n
31
LEU
31
A
LEU
32
n
32
LEU
32
A
ALA
33
n
33
ALA
33
A
HIS
34
n
34
HIS
34
A
SER
35
n
35
SER
35
A
ASP
36
n
36
ASP
36
A
GLY
37
n
37
GLY
37
A
ASP
38
n
38
ASP
38
A
VAL
39
n
39
VAL
39
A
ALA
40
n
40
ALA
40
A
LEU
41
n
41
LEU
41
A
HIS
42
n
42
HIS
42
A
ALA
43
n
43
ALA
43
A
LEU
44
n
44
LEU
44
A
THR
45
n
45
THR
45
A
ASP
46
n
46
ASP
46
A
ALA
47
n
47
ALA
47
A
LEU
48
n
48
LEU
48
A
LEU
49
n
49
LEU
49
A
GLY
50
n
50
GLY
50
A
ALA
51
n
51
ALA
51
A
ALA
52
n
52
ALA
52
A
ALA
53
n
53
ALA
53
A
LEU
54
n
54
LEU
54
A
GLY
55
n
55
GLY
55
A
ASP
56
n
56
ASP
56
A
ILE
57
n
57
ILE
57
A
GLY
58
n
58
GLY
58
A
LYS
59
n
59
LYS
59
A
LEU
60
n
60
LEU
60
A
PHE
61
n
61
PHE
61
A
PRO
62
n
62
PRO
62
A
ASP
63
n
63
ASP
63
A
THR
64
n
64
THR
64
A
ASP
65
n
65
ASP
65
A
PRO
66
n
66
PRO
66
A
ALA
67
n
67
ALA
67
A
PHE
68
n
68
PHE
68
A
LYS
69
n
69
LYS
69
A
GLY
70
n
70
GLY
70
A
ALA
71
n
71
ALA
71
A
ASP
72
n
72
ASP
72
A
SER
73
n
73
SER
73
A
ARG
74
n
74
ARG
74
A
GLU
75
n
75
GLU
75
A
LEU
76
n
76
LEU
76
A
LEU
77
n
77
LEU
77
A
ARG
78
n
78
ARG
78
A
GLU
79
n
79
GLU
79
A
ALA
80
n
80
ALA
80
A
TRP
81
n
81
TRP
81
A
ARG
82
n
82
ARG
82
A
ARG
83
n
83
ARG
83
A
ILE
84
n
84
ILE
84
A
GLN
85
n
85
GLN
85
A
ALA
86
n
86
ALA
86
A
LYS
87
n
87
LYS
87
A
GLY
88
n
88
GLY
88
A
TYR
89
n
89
TYR
89
A
THR
90
n
90
THR
90
A
LEU
91
n
91
LEU
91
A
GLY
92
n
92
GLY
92
A
ASN
93
n
93
ASN
93
A
VAL
94
n
94
VAL
94
A
ASP
95
n
95
ASP
95
A
VAL
96
n
96
VAL
96
A
THR
97
n
97
THR
97
A
ILE
98
n
98
ILE
98
A
ILE
99
n
99
ILE
99
A
ALA
100
n
100
ALA
100
A
GLN
101
n
101
GLN
101
A
ALA
102
n
102
ALA
102
A
PRO
103
n
103
PRO
103
A
LYS
104
n
104
LYS
104
A
MET
105
n
105
MET
105
A
LEU
106
n
106
LEU
106
A
PRO
107
n
107
PRO
107
A
HIS
108
n
108
HIS
108
A
ILE
109
n
109
ILE
109
A
PRO
110
n
110
PRO
110
A
GLN
111
n
111
GLN
111
A
MET
112
n
112
MET
112
A
ARG
113
n
113
ARG
113
A
VAL
114
n
114
VAL
114
A
PHE
115
n
115
PHE
115
A
ILE
116
n
116
ILE
116
A
ALA
117
n
117
ALA
117
A
GLU
118
n
118
GLU
118
A
ASP
119
n
119
ASP
119
A
LEU
120
n
120
LEU
120
A
GLY
121
n
121
GLY
121
A
CYS
122
n
122
CYS
122
A
HIS
123
n
123
HIS
123
A
MET
124
n
124
MET
124
A
ASP
125
n
125
ASP
125
A
ASP
126
n
126
ASP
126
A
VAL
127
n
127
VAL
127
A
ASN
128
n
128
ASN
128
A
VAL
129
n
129
VAL
129
A
LYS
130
n
130
LYS
130
A
ALA
131
n
131
ALA
131
A
THR
132
n
132
THR
132
A
THR
133
n
133
THR
133
A
THR
134
n
134
THR
134
A
GLU
135
n
135
GLU
135
A
LYS
136
n
136
LYS
136
A
LEU
137
n
137
LEU
137
A
GLY
138
n
138
GLY
138
A
PHE
139
n
139
PHE
139
A
THR
140
n
140
THR
140
A
GLY
141
n
141
GLY
141
A
ARG
142
n
142
ARG
142
A
GLY
143
n
143
GLY
143
A
GLU
144
n
144
GLU
144
A
GLY
145
n
145
GLY
145
A
ILE
146
n
146
ILE
146
A
ALA
147
n
147
ALA
147
A
CYS
148
n
148
CYS
148
A
GLU
149
n
149
GLU
149
A
ALA
150
n
150
ALA
150
A
VAL
151
n
151
VAL
151
A
ALA
152
n
152
ALA
152
A
LEU
153
n
153
LEU
153
A
LEU
154
n
154
LEU
154
A
ILE
155
n
155
ILE
155
A
LYS
156
n
156
LYS
156
A
n
157
157
A
n
158
158
A
n
159
159
A
author_and_software_defined_assembly
PISA,PQS
3
trimeric
5720
-34
18090
A
ASP
8
A
OD2
ASP
8
1_555
A
MN
201
B
MN
MN
1_555
A
HIS
10
A
NE2
HIS
10
1_555
109.5
A
ASP
8
A
OD2
ASP
8
1_555
A
MN
201
B
MN
MN
1_555
A
HIS
42
A
ND1
HIS
42
1_555
83.3
A
HIS
10
A
NE2
HIS
10
1_555
A
MN
201
B
MN
MN
1_555
A
HIS
42
A
ND1
HIS
42
1_555
109.1
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
0.0000000000
0.0000000000
1.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
5_555
z,x,y
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1.0000000000
0.0000000000
0.0000000000
9_555
y,z,x
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
A
N
GLY
6
A
N
GLY
6
A
O
ALA
150
A
O
ALA
150
A
O
GLU
149
A
O
GLU
149
A
N
THR
97
A
N
THR
97
A
N
ILE
98
A
N
ILE
98
A
O
LYS
130
A
O
LYS
130
A
N
ILE
18
A
N
ILE
18
A
O
ILE
25
A
O
ILE
25
1
A
HOH
202
C
HOH
1
A
HOH
206
C
HOH
1
A
ALA
157
A
ALA
157
1
Y
1
A
THR
158
A
THR
158
1
Y
1
A
LYS
159
A
LYS
159
1
Y
1
25.52
2.70
111.00
136.52
A
A
A
N
CA
C
ILE
ILE
ILE
155
155
155
N
1
18.13
2.70
111.00
129.13
A
A
A
N
CA
C
LYS
LYS
LYS
156
156
156
N
1
A
GLU
15
52.63
-91.03
1
A
TYR
27
-174.02
148.37
1
A
LEU
32
-64.68
-122.97
1
A
ALA
33
68.18
134.52
1
A
SER
35
167.44
154.47
1
A
ASP
56
-173.07
57.19
1
A
ILE
57
51.95
79.59
1
A
PRO
62
-64.66
-109.02
1
A
ASP
63
-169.67
-31.79
1
A
PRO
66
-50.68
1.49
1
A
ALA
67
-63.42
-75.51
1
A
LYS
69
-79.32
-81.17
1
A
CYS
122
50.15
164.90
1
A
THR
134
82.20
-7.73
1
A
LEU
137
-103.74
-71.20
PROTEIN_REP.PARAM
PROTEIN.TOP
WATER_REP.PARAM
WATER.TOP
ION.PARAM
ION.TOP
72.3
.33
.00
.00
-.16
.00
-.16
0.2490000
.008
0.2320000
2.80
24.74
1088
22633
22633
4.8
94.7
RANDOM
623227.17
.000000
1
RESTRAINED
THROUGHOUT
0.0
Rigid body
PDB ENTRY 1KNJ
Engh & Huber
FLAT MODEL
58.3984
.369238
.41
.39
5.00
.50
.54
2.80
24.74
11
1178
1
0
1166
.010
1.8
24.4
.84
0.3670000
.027
0.3660000
2.98
187
3179
3179
6
5.6
84.3
111.6
2.80
30.00
1KNK
24117
24117
1
0
0.0910000
1
15.7
3.54
93.6
2.80
2.90
5.0
404
0.4150000
1
3.3
96.9
refinement
CNS
data reduction
DENZO
data scaling
SCALEPACK
phasing
CNS
Crystal Structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate Synthase (ispF) from E. coli involved in Mevalonate-Independent Isoprenoid Biosynthesis
1
N
N
2
N
N
3
N
N
The biological assembly is a homotrimer generated from the monomer
in the asymmetric unit by the operations: z,x,y and y,z,x
A
ASP
38
A
ASP
38
HELX_P
A
ALA
53
A
ALA
53
1
1
16
A
ASP
72
A
ASP
72
HELX_P
A
LYS
87
A
LYS
87
1
2
16
A
MET
105
A
MET
105
HELX_P
A
PRO
107
A
PRO
107
5
3
3
A
HIS
108
A
HIS
108
HELX_P
A
ALA
117
A
ALA
117
1
4
10
A
HIS
123
A
HIS
123
HELX_P
A
ASP
125
A
ASP
125
5
5
3
metalc
2.339
A
ASP
8
A
OD2
ASP
8
1_555
A
MN
201
B
MN
MN
1_555
metalc
2.719
A
HIS
10
A
NE2
HIS
10
1_555
A
MN
201
B
MN
MN
1_555
metalc
2.457
A
HIS
42
A
ND1
HIS
42
1_555
A
MN
201
B
MN
MN
1_555
METAL BINDING PROTEIN
isoprenoids, deoxyxylulose/methyl-erythritol-phosphate pathway, cyclodiphosphate, MEP, YgbB, ispF, MECDP, 2-C-methyl-D-erythritol-2, 4-cyclodiphosphate synthase, METAL BINDING PROTEIN
A
ALA
102
A
ALA
102
1
A
PRO
103
A
PRO
103
-1.77
ISPF_ECOLI
UNP
1
1
P62617
MRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREA
WRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLIKATK
1
159
1KNK
1
159
P62617
A
1
1
159
4
2
anti-parallel
anti-parallel
parallel
anti-parallel
A
ARG
2
A
ARG
2
A
ALA
11
A
ALA
11
A
GLY
145
A
GLY
145
A
LEU
154
A
LEU
154
A
ASN
93
A
ASN
93
A
ILE
99
A
ILE
99
A
VAL
127
A
VAL
127
A
THR
132
A
THR
132
A
ILE
18
A
ILE
18
A
ILE
20
A
ILE
20
A
VAL
23
A
VAL
23
A
ILE
25
A
ILE
25
BINDING SITE FOR RESIDUE MN A 201
A
MN
201
Software
3
A
ASP
8
A
ASP
8
3
1_555
A
HIS
10
A
HIS
10
3
1_555
A
HIS
42
A
HIS
42
3
1_555
199
I 21 3