.006932
.000000
.000000
.000000
.006932
.000000
.000000
.000000
.006932
.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
144.254
144.254
144.254
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
C9 H14 N3 O8 P
323.197
CYTIDINE-5'-MONOPHOSPHATE
non-polymer
C5 H12 O9 P2
278.091
2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE
non-polymer
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
C5 H11 N O2 Se
196.106
n
SELENOMETHIONINE
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
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
1.000000
.000000
.000000
.000000
1.000000
.000000
.000000
.000000
1.000000
.00000
.00000
.00000
100
1
1
1
mirrors
CCD
2001-03-26
MARRESEARCH
HORIZONTALLY FOCUSED BY SAGITTAL CURVED 2nd CRYSTAL
MAD
M
x-ray
1
SAGITALLY FOCUSED Ge(220)
SINGLE WAVELENGTH
M
x-ray
1
0.9795
1.0
0.9800
1.0
0.9724
1.0
0.9340
1.0
BM30A
ESRF
0.9795, 0.9800, 0.9724
SYNCHROTRON
ESRF BEAMLINE BM30A
ID14-1
ESRF
0.9340
SYNCHROTRON
ESRF BEAMLINE ID14-1
17108.113
2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
1
man
polymer
54.938
MANGANESE (II) ION
1
syn
non-polymer
323.197
CYTIDINE-5'-MONOPHOSPHATE
1
syn
non-polymer
278.091
2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE
1
syn
non-polymer
18.015
water
22
nat
water
MECPS
no
yes
(MSE)RIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSREL
LREAWRRIQAKGYTLGNVDVTIIAQAPK(MSE)LPHIPQ(MSE)RVFIAEDLGCH(MSE)DDVNVKATTTEKLGFTGRGE
GIACEAVALLIKATK
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
repository
Initial release
Version format compliance
Derived calculations
Version format compliance
1
0
2002-06-18
1
1
2008-04-27
1
2
2011-07-13
Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (ispF) from E. coli involved in
mevalonate-independent isoprenoid biosynthesis
RCSB
Y
RCSB
2001-12-18
REL
REL
MN
MANGANESE (II) ION
C5P
CYTIDINE-5'-MONOPHOSPHATE
CDI
2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE
HOH
water
MN
1
2
MN
MN
401
A
C5P
1
3
C5P
C5P
201
A
PBB
1
4
CDI
CDI
301
A
HOH
1
5
HOH
HOH
402
A
HOH
2
5
HOH
HOH
403
A
HOH
3
5
HOH
HOH
404
A
HOH
4
5
HOH
HOH
405
A
HOH
5
5
HOH
HOH
406
A
HOH
6
5
HOH
HOH
407
A
HOH
7
5
HOH
HOH
408
A
HOH
8
5
HOH
HOH
409
A
HOH
9
5
HOH
HOH
410
A
HOH
10
5
HOH
HOH
411
A
HOH
11
5
HOH
HOH
412
A
HOH
12
5
HOH
HOH
413
A
HOH
13
5
HOH
HOH
414
A
HOH
14
5
HOH
HOH
415
A
HOH
15
5
HOH
HOH
416
A
HOH
16
5
HOH
HOH
417
A
HOH
17
5
HOH
HOH
418
A
HOH
18
5
HOH
HOH
419
A
HOH
19
5
HOH
HOH
420
A
HOH
20
5
HOH
HOH
421
A
HOH
21
5
HOH
HOH
422
A
HOH
22
5
HOH
HOH
423
A
MSE
1
n
1
MSE
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
MSE
105
n
105
MSE
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
MSE
112
n
112
MSE
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
MSE
124
n
124
MSE
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
9660
-46
16120
A
ASP
8
A
OD1
ASP
8
1_555
A
MN
401
B
MN
MN
1_555
A
ASP
8
A
OD2
ASP
8
1_555
55.0
A
MSE
1
SELENOMETHIONINE
A
MSE
1
MET
A
MSE
105
SELENOMETHIONINE
A
MSE
105
MET
A
MSE
112
SELENOMETHIONINE
A
MSE
112
MET
A
MSE
124
SELENOMETHIONINE
A
MSE
124
MET
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
ALA
147
A
O
ALA
147
A
N
ILE
99
A
N
ILE
99
A
N
VAL
94
A
N
VAL
94
A
O
ASN
128
A
O
ASN
128
A
N
ILE
18
A
N
ILE
18
A
O
ILE
25
A
O
ILE
25
1
A
HOH
403
E
HOH
1
A
HOH
413
E
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
11.87
1.50
119.30
131.17
A
A
A
C
N
CA
GLY
PRO
PRO
16
17
17
Y
1
20.97
1.50
119.30
140.27
A
A
A
C
N
CA
PHE
PRO
PRO
61
62
62
Y
1
-25.39
2.10
128.40
103.01
A
A
A
C
N
CD
PHE
PRO
PRO
61
62
62
Y
1
A
ASP
8
-170.55
145.07
1
A
GLU
15
-65.48
-130.65
1
A
PRO
17
-20.50
139.88
1
A
TYR
27
-172.94
140.67
1
A
ASP
56
33.54
169.16
1
A
PHE
61
64.00
158.96
1
A
PRO
62
-142.13
35.26
1
A
THR
64
38.74
57.53
1
A
PRO
66
-14.03
86.25
1
A
ALA
67
172.42
-61.07
1
A
LYS
69
153.84
119.68
1
A
LYS
87
-80.53
31.14
PROTEIN_REP.PARAM
PROTEIN.TOP
WATER_REP.PARAM
WATER.TOP
ION.PARAM
ION.TOP
LIGAND.PARAM
LIGAND.TOP
62.6
.00
.00
.00
.00
.00
.00
0.2500000
.010
0.2410000
0.2860000
2.80
14.71
577
12817
11262
5.1
87.9
RANDOM
1949090.32
.000000
1
RESTRAINED
THROUGHOUT
2.0
MAD
Engh & Huber
FLAT MODEL
41.9833
.333926
.39
.37
5.00
.38
.46
2.80
14.71
22
1226
38
0
1166
.010
1.8
23.6
1.52
0.3700000
.038
0.3340000
2.98
76
1495
1495
6
4.8
75.1
92.0
2.7
99.0
1KNJ
11923
11923
1
1
0.0400000
0.0660000
1,2
19
4.1
99.3
0.6600000
2.80
2.87
482.0
1579
1,2
4.1
100.0
refinement
CNS
data reduction
DENZO
data scaling
SCALEPACK
phasing
CNS
2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
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+
1
N
N
2
N
N
3
N
N
4
N
N
5
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
52
A
ALA
52
1
1
15
A
ASP
56
A
ASP
56
HELX_P
A
PHE
61
A
PHE
61
5
2
6
A
ASP
72
A
ASP
72
HELX_P
A
LYS
87
A
LYS
87
1
3
16
A
HIS
108
A
HIS
108
HELX_P
A
LEU
120
A
LEU
120
1
4
13
A
HIS
123
A
HIS
123
HELX_P
A
ASP
125
A
ASP
125
5
5
3
A
LEU
137
A
LEU
137
HELX_P
A
ARG
142
A
ARG
142
1
6
6
covale
1.330
A
MSE
1
A
C
MSE
1
1_555
A
ARG
2
A
N
ARG
2
1_555
covale
1.328
A
LYS
104
A
C
LYS
104
1_555
A
MSE
105
A
N
MSE
105
1_555
covale
1.329
A
MSE
105
A
C
MSE
105
1_555
A
LEU
106
A
N
LEU
106
1_555
covale
1.339
A
GLN
111
A
C
GLN
111
1_555
A
MSE
112
A
N
MSE
112
1_555
covale
1.327
A
MSE
112
A
C
MSE
112
1_555
A
ARG
113
A
N
ARG
113
1_555
covale
1.323
A
HIS
123
A
C
HIS
123
1_555
A
MSE
124
A
N
MSE
124
1_555
covale
1.328
A
MSE
124
A
C
MSE
124
1_555
A
ASP
125
A
N
ASP
125
1_555
metalc
2.487
A
ASP
8
A
OD1
ASP
8
1_555
A
MN
401
B
MN
MN
1_555
metalc
2.298
A
ASP
8
A
OD2
ASP
8
1_555
A
MN
401
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
-0.66
ISPF_ECOLI
UNP
1
1
P62617
MRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREA
WRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLIKATK
1
159
1KNJ
1
159
P62617
A
1
1
159
1
MET
MODIFIED RESIDUE
MSE
1
1KNJ
A
P62617
UNP
1
1
1
MET
MODIFIED RESIDUE
MSE
105
1KNJ
A
P62617
UNP
105
105
1
MET
MODIFIED RESIDUE
MSE
112
1KNJ
A
P62617
UNP
112
112
1
MET
MODIFIED RESIDUE
MSE
124
1KNJ
A
P62617
UNP
124
124
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
ILE
155
A
ILE
155
A
THR
90
A
THR
90
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 401
Software
4
BINDING SITE FOR RESIDUE C5P A 201
Software
12
BINDING SITE FOR RESIDUE CDI A 301
Software
11
A
ASP
8
A
ASP
8
4
1_555
A
HIS
10
A
HIS
10
4
1_555
A
HIS
42
A
HIS
42
4
1_555
A
CDI
301
D
CDI
4
5_555
A
ASP
56
A
ASP
56
12
9_555
A
GLY
58
A
GLY
58
12
9_555
A
ALA
100
A
ALA
100
12
1_555
A
PRO
103
A
PRO
103
12
1_555
A
LYS
104
A
LYS
104
12
1_555
A
MSE
105
A
MSE
105
12
1_555
A
LEU
106
A
LEU
106
12
1_555
A
ALA
131
A
ALA
131
12
1_555
A
THR
132
A
THR
132
12
1_555
A
THR
133
A
THR
133
12
1_555
A
GLU
135
A
GLU
135
12
1_555
A
CDI
301
D
CDI
12
1_555
A
ASP
8
A
ASP
8
11
9_555
A
HIS
10
A
HIS
10
11
9_555
A
ALA
33
A
ALA
33
11
9_555
A
HIS
34
A
HIS
34
11
9_555
A
SER
35
A
SER
35
11
9_555
A
HIS
42
A
HIS
42
11
9_555
A
ILE
57
A
ILE
57
11
9_555
A
PRO
62
A
PRO
62
11
9_555
A
C5P
201
C
C5P
11
1_555
A
MN
401
B
MN
11
9_555
A
HOH
422
E
HOH
11
1_555
199
I 21 3