.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