0.008326 0.004807 0.000000 0.000000 0.009614 0.000000 0.000000 0.000000 0.019037 0.00000 0.00000 0.00000 Xu, K. Dedic, E. Brodersen, D.E. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 18 90.00 90.00 120.00 120.100 120.100 52.530 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 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 Proteins PSFGEY 0867 1097-0134 84 892 899 10.1002/prot.25002 26833558 Structural analysis of the active site architecture of the VapC toxin from Shigella flexneri. 2016 100 1 CCD 2013-12-12 MARMOSAIC 225 mm CCD SINGLE WAVELENGTH M x-ray 1 0.9795 1.0 I911-3 MAX II 0.9795 SYNCHROTRON MAX II BEAMLINE I911-3 15620.947 tRNA(fMet)-specific endonuclease VapC 3.1.-.- D7A 2 man polymer 18.015 water 98 nat water RNase VapC,Toxin VapC no no MHHHHHHLKFMLATNICIFTIKNKPASVRERFNLNQGKMCISSVTLMELIYGAEKSQMPERNLAVIEGFVSRIDVLDYDA AAATHTGQIRAELARQGRPVGPFDQMIAGHARSRGLIIVTNNTREFERVGGLRTEDWS MHHHHHHLKFMLATNICIFTIKNKPASVRERFNLNQGKMCISSVTLMELIYGAEKSQMPERNLAVIEGFVSRIDVLDYDA AAATHTGQIRAELARQGRPVGPFDQMIAGHARSRGLIIVTNNTREFERVGGLRTEDWS A,B 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 sample 1 138 vapC, mvpA, stborf2, CP0245 623 Shigella flexneri 469008 Escherichia coli BL21(DE3) Biological sequence 1 2.33 47.15 VAPOR DIFFUSION, SITTING DROP 7.0 0.2 M sodium malonate, 20% PEG 3350 292.15 diffrn_source repository Initial release Database references Data collection 1 0 2016-02-17 1 1 2016-06-15 1 2 2018-01-17 _diffrn_source.pdbx_synchrotron_site China Chinese Scholarship Council 5ECD contains the same protein with a different mutation N RCSB Y PDBE 2015-10-20 REL REL HOH water HOH 73 2 HOH HOH 201 A HOH 70 2 HOH HOH 202 A HOH 134 2 HOH HOH 203 A HOH 74 2 HOH HOH 204 A HOH 36 2 HOH HOH 205 A HOH 131 2 HOH HOH 206 A HOH 66 2 HOH HOH 207 A HOH 2 2 HOH HOH 208 A HOH 81 2 HOH HOH 209 A HOH 3 2 HOH HOH 210 A HOH 1 2 HOH HOH 211 A HOH 5 2 HOH HOH 212 A HOH 114 2 HOH HOH 213 A HOH 29 2 HOH HOH 214 A HOH 40 2 HOH HOH 215 A HOH 69 2 HOH HOH 216 A HOH 10 2 HOH HOH 217 A HOH 95 2 HOH HOH 218 A HOH 110 2 HOH HOH 219 A HOH 44 2 HOH HOH 220 A HOH 26 2 HOH HOH 221 A HOH 15 2 HOH HOH 222 A HOH 12 2 HOH HOH 223 A HOH 27 2 HOH HOH 224 A HOH 117 2 HOH HOH 225 A HOH 124 2 HOH HOH 226 A HOH 8 2 HOH HOH 227 A HOH 122 2 HOH HOH 228 A HOH 21 2 HOH HOH 229 A HOH 86 2 HOH HOH 230 A HOH 87 2 HOH HOH 231 A HOH 79 2 HOH HOH 232 A HOH 41 2 HOH HOH 233 A HOH 17 2 HOH HOH 234 A HOH 46 2 HOH HOH 235 A HOH 64 2 HOH HOH 236 A HOH 48 2 HOH HOH 237 A HOH 85 2 HOH HOH 238 A HOH 6 2 HOH HOH 239 A HOH 72 2 HOH HOH 240 A HOH 39 2 HOH HOH 241 A HOH 28 2 HOH HOH 242 A HOH 4 2 HOH HOH 243 A HOH 129 2 HOH HOH 244 A HOH 23 2 HOH HOH 245 A HOH 84 2 HOH HOH 246 A HOH 42 2 HOH HOH 247 A HOH 127 2 HOH HOH 248 A HOH 130 2 HOH HOH 249 A HOH 24 2 HOH HOH 250 A HOH 80 2 HOH HOH 251 A HOH 9 2 HOH HOH 252 A HOH 22 2 HOH HOH 253 A HOH 123 2 HOH HOH 254 A HOH 62 2 HOH HOH 255 A HOH 126 2 HOH HOH 256 A HOH 88 2 HOH HOH 257 A HOH 68 2 HOH HOH 258 A HOH 33 2 HOH HOH 259 A HOH 55 2 HOH HOH 260 A HOH 37 2 HOH HOH 261 A HOH 38 2 HOH HOH 262 A HOH 75 2 HOH HOH 263 A HOH 35 2 HOH HOH 264 A HOH 71 2 HOH HOH 265 A HOH 113 2 HOH HOH 266 A HOH 94 2 HOH HOH 267 A HOH 7 2 HOH HOH 268 A HOH 67 2 HOH HOH 269 A HOH 90 2 HOH HOH 270 A HOH 50 2 HOH HOH 271 A HOH 128 2 HOH HOH 272 A HOH 120 2 HOH HOH 273 A HOH 107 2 HOH HOH 274 A HOH 57 2 HOH HOH 275 A HOH 13 2 HOH HOH 276 A HOH 11 2 HOH HOH 201 B HOH 78 2 HOH HOH 202 B HOH 133 2 HOH HOH 203 B HOH 14 2 HOH HOH 204 B HOH 61 2 HOH HOH 205 B HOH 34 2 HOH HOH 206 B HOH 83 2 HOH HOH 207 B HOH 63 2 HOH HOH 208 B HOH 65 2 HOH HOH 209 B HOH 60 2 HOH HOH 210 B HOH 31 2 HOH HOH 211 B HOH 20 2 HOH HOH 212 B HOH 100 2 HOH HOH 213 B HOH 109 2 HOH HOH 214 B HOH 54 2 HOH HOH 215 B HOH 25 2 HOH HOH 216 B HOH 108 2 HOH HOH 217 B HOH 56 2 HOH HOH 218 B HOH 82 2 HOH HOH 219 B HOH 58 2 HOH HOH 220 B HOH 32 2 HOH HOH 221 B HOH 59 2 HOH HOH 222 B n 1 -5 A n 2 -4 A n 3 -3 A n 4 -2 A n 5 -1 A n 6 0 A HIS 1 n 7 HIS 1 A LEU 2 n 8 LEU 2 A LYS 3 n 9 LYS 3 A PHE 4 n 10 PHE 4 A MET 5 n 11 MET 5 A LEU 6 n 12 LEU 6 A ALA 7 n 13 ALA 7 A THR 8 n 14 THR 8 A ASN 9 n 15 ASN 9 A ILE 10 n 16 ILE 10 A CYS 11 n 17 CYS 11 A ILE 12 n 18 ILE 12 A PHE 13 n 19 PHE 13 A THR 14 n 20 THR 14 A ILE 15 n 21 ILE 15 A LYS 16 n 22 LYS 16 A ASN 17 n 23 ASN 17 A LYS 18 n 24 LYS 18 A PRO 19 n 25 PRO 19 A ALA 20 n 26 ALA 20 A SER 21 n 27 SER 21 A VAL 22 n 28 VAL 22 A ARG 23 n 29 ARG 23 A GLU 24 n 30 GLU 24 A ARG 25 n 31 ARG 25 A PHE 26 n 32 PHE 26 A ASN 27 n 33 ASN 27 A LEU 28 n 34 LEU 28 A ASN 29 n 35 ASN 29 A GLN 30 n 36 GLN 30 A GLY 31 n 37 GLY 31 A LYS 32 n 38 LYS 32 A MET 33 n 39 MET 33 A CYS 34 n 40 CYS 34 A ILE 35 n 41 ILE 35 A SER 36 n 42 SER 36 A SER 37 n 43 SER 37 A VAL 38 n 44 VAL 38 A THR 39 n 45 THR 39 A LEU 40 n 46 LEU 40 A MET 41 n 47 MET 41 A GLU 42 n 48 GLU 42 A LEU 43 n 49 LEU 43 A ILE 44 n 50 ILE 44 A TYR 45 n 51 TYR 45 A GLY 46 n 52 GLY 46 A ALA 47 n 53 ALA 47 A GLU 48 n 54 GLU 48 A LYS 49 n 55 LYS 49 A SER 50 n 56 SER 50 A GLN 51 n 57 GLN 51 A MET 52 n 58 MET 52 A PRO 53 n 59 PRO 53 A GLU 54 n 60 GLU 54 A ARG 55 n 61 ARG 55 A ASN 56 n 62 ASN 56 A LEU 57 n 63 LEU 57 A ALA 58 n 64 ALA 58 A VAL 59 n 65 VAL 59 A ILE 60 n 66 ILE 60 A GLU 61 n 67 GLU 61 A GLY 62 n 68 GLY 62 A PHE 63 n 69 PHE 63 A VAL 64 n 70 VAL 64 A SER 65 n 71 SER 65 A ARG 66 n 72 ARG 66 A ILE 67 n 73 ILE 67 A ASP 68 n 74 ASP 68 A VAL 69 n 75 VAL 69 A LEU 70 n 76 LEU 70 A ASP 71 n 77 ASP 71 A TYR 72 n 78 TYR 72 A ASP 73 n 79 ASP 73 A ALA 74 n 80 ALA 74 A ALA 75 n 81 ALA 75 A ALA 76 n 82 ALA 76 A ALA 77 n 83 ALA 77 A THR 78 n 84 THR 78 A HIS 79 n 85 HIS 79 A THR 80 n 86 THR 80 A GLY 81 n 87 GLY 81 A GLN 82 n 88 GLN 82 A ILE 83 n 89 ILE 83 A ARG 84 n 90 ARG 84 A ALA 85 n 91 ALA 85 A GLU 86 n 92 GLU 86 A LEU 87 n 93 LEU 87 A ALA 88 n 94 ALA 88 A ARG 89 n 95 ARG 89 A GLN 90 n 96 GLN 90 A GLY 91 n 97 GLY 91 A ARG 92 n 98 ARG 92 A PRO 93 n 99 PRO 93 A VAL 94 n 100 VAL 94 A GLY 95 n 101 GLY 95 A PRO 96 n 102 PRO 96 A PHE 97 n 103 PHE 97 A ASP 98 n 104 ASP 98 A GLN 99 n 105 GLN 99 A MET 100 n 106 MET 100 A ILE 101 n 107 ILE 101 A ALA 102 n 108 ALA 102 A GLY 103 n 109 GLY 103 A HIS 104 n 110 HIS 104 A ALA 105 n 111 ALA 105 A ARG 106 n 112 ARG 106 A SER 107 n 113 SER 107 A ARG 108 n 114 ARG 108 A GLY 109 n 115 GLY 109 A LEU 110 n 116 LEU 110 A ILE 111 n 117 ILE 111 A ILE 112 n 118 ILE 112 A VAL 113 n 119 VAL 113 A THR 114 n 120 THR 114 A ASN 115 n 121 ASN 115 A ASN 116 n 122 ASN 116 A THR 117 n 123 THR 117 A ARG 118 n 124 ARG 118 A GLU 119 n 125 GLU 119 A PHE 120 n 126 PHE 120 A GLU 121 n 127 GLU 121 A ARG 122 n 128 ARG 122 A VAL 123 n 129 VAL 123 A GLY 124 n 130 GLY 124 A GLY 125 n 131 GLY 125 A LEU 126 n 132 LEU 126 A ARG 127 n 133 ARG 127 A THR 128 n 134 THR 128 A GLU 129 n 135 GLU 129 A ASP 130 n 136 ASP 130 A TRP 131 n 137 TRP 131 A SER 132 n 138 SER 132 A n 1 -5 B n 2 -4 B n 3 -3 B n 4 -2 B n 5 -1 B n 6 0 B HIS 1 n 7 HIS 1 B LEU 2 n 8 LEU 2 B LYS 3 n 9 LYS 3 B PHE 4 n 10 PHE 4 B MET 5 n 11 MET 5 B LEU 6 n 12 LEU 6 B ALA 7 n 13 ALA 7 B THR 8 n 14 THR 8 B ASN 9 n 15 ASN 9 B ILE 10 n 16 ILE 10 B CYS 11 n 17 CYS 11 B ILE 12 n 18 ILE 12 B PHE 13 n 19 PHE 13 B THR 14 n 20 THR 14 B ILE 15 n 21 ILE 15 B LYS 16 n 22 LYS 16 B ASN 17 n 23 ASN 17 B LYS 18 n 24 LYS 18 B n 25 19 B n 26 20 B n 27 21 B n 28 22 B n 29 23 B n 30 24 B n 31 25 B n 32 26 B n 33 27 B LEU 28 n 34 LEU 28 B ASN 29 n 35 ASN 29 B GLN 30 n 36 GLN 30 B GLY 31 n 37 GLY 31 B LYS 32 n 38 LYS 32 B MET 33 n 39 MET 33 B CYS 34 n 40 CYS 34 B ILE 35 n 41 ILE 35 B SER 36 n 42 SER 36 B SER 37 n 43 SER 37 B VAL 38 n 44 VAL 38 B THR 39 n 45 THR 39 B LEU 40 n 46 LEU 40 B MET 41 n 47 MET 41 B GLU 42 n 48 GLU 42 B LEU 43 n 49 LEU 43 B ILE 44 n 50 ILE 44 B TYR 45 n 51 TYR 45 B GLY 46 n 52 GLY 46 B ALA 47 n 53 ALA 47 B GLU 48 n 54 GLU 48 B LYS 49 n 55 LYS 49 B SER 50 n 56 SER 50 B GLN 51 n 57 GLN 51 B MET 52 n 58 MET 52 B PRO 53 n 59 PRO 53 B GLU 54 n 60 GLU 54 B ARG 55 n 61 ARG 55 B ASN 56 n 62 ASN 56 B LEU 57 n 63 LEU 57 B ALA 58 n 64 ALA 58 B VAL 59 n 65 VAL 59 B ILE 60 n 66 ILE 60 B GLU 61 n 67 GLU 61 B GLY 62 n 68 GLY 62 B PHE 63 n 69 PHE 63 B VAL 64 n 70 VAL 64 B SER 65 n 71 SER 65 B ARG 66 n 72 ARG 66 B ILE 67 n 73 ILE 67 B ASP 68 n 74 ASP 68 B VAL 69 n 75 VAL 69 B LEU 70 n 76 LEU 70 B ASP 71 n 77 ASP 71 B TYR 72 n 78 TYR 72 B ASP 73 n 79 ASP 73 B ALA 74 n 80 ALA 74 B ALA 75 n 81 ALA 75 B ALA 76 n 82 ALA 76 B ALA 77 n 83 ALA 77 B THR 78 n 84 THR 78 B HIS 79 n 85 HIS 79 B THR 80 n 86 THR 80 B GLY 81 n 87 GLY 81 B GLN 82 n 88 GLN 82 B ILE 83 n 89 ILE 83 B ARG 84 n 90 ARG 84 B ALA 85 n 91 ALA 85 B GLU 86 n 92 GLU 86 B LEU 87 n 93 LEU 87 B ALA 88 n 94 ALA 88 B ARG 89 n 95 ARG 89 B GLN 90 n 96 GLN 90 B GLY 91 n 97 GLY 91 B ARG 92 n 98 ARG 92 B PRO 93 n 99 PRO 93 B VAL 94 n 100 VAL 94 B GLY 95 n 101 GLY 95 B PRO 96 n 102 PRO 96 B PHE 97 n 103 PHE 97 B ASP 98 n 104 ASP 98 B GLN 99 n 105 GLN 99 B MET 100 n 106 MET 100 B ILE 101 n 107 ILE 101 B ALA 102 n 108 ALA 102 B GLY 103 n 109 GLY 103 B HIS 104 n 110 HIS 104 B ALA 105 n 111 ALA 105 B ARG 106 n 112 ARG 106 B SER 107 n 113 SER 107 B ARG 108 n 114 ARG 108 B GLY 109 n 115 GLY 109 B LEU 110 n 116 LEU 110 B ILE 111 n 117 ILE 111 B ILE 112 n 118 ILE 112 B VAL 113 n 119 VAL 113 B THR 114 n 120 THR 114 B ASN 115 n 121 ASN 115 B ASN 116 n 122 ASN 116 B THR 117 n 123 THR 117 B ARG 118 n 124 ARG 118 B GLU 119 n 125 GLU 119 B PHE 120 n 126 PHE 120 B GLU 121 n 127 GLU 121 B ARG 122 n 128 ARG 122 B VAL 123 n 129 VAL 123 B GLY 124 n 130 GLY 124 B GLY 125 n 131 GLY 125 B LEU 126 n 132 LEU 126 B ARG 127 n 133 ARG 127 B THR 128 n 134 THR 128 B GLU 129 n 135 GLU 129 B ASP 130 n 136 ASP 130 B TRP 131 n 137 TRP 131 B SER 132 n 138 SER 132 B 7.2223 0.3473 -2.3881 1.6086 -0.0421 2.8054 -0.6098 -0.3808 -0.3815 0.1388 0.2567 0.0487 0.3384 0.2283 0.2280 0.3183 0.0841 -0.0215 0.2823 -0.0277 0.2039 refined -23.8041 -7.3765 13.5334 X-RAY DIFFRACTION X-RAY DIFFRACTION 1 all author_and_software_defined_assembly PISA 2 dimeric 2210 -21 11650 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 A O LEU 70 A O LEU 76 A N ILE 35 A N ILE 41 A O CYS 34 A O CYS 40 A N LEU 6 A N LEU 12 A N MET 5 A N MET 11 A O ILE 111 A O ILE 117 A N ILE 112 A N ILE 118 A O GLU 129 A O GLU 135 B O LEU 70 B O LEU 76 B N ILE 35 B N ILE 41 B O CYS 34 B O CYS 40 B N LEU 6 B N LEU 12 B N MET 5 B N MET 11 B O ILE 111 B O ILE 117 B N ILE 112 B N ILE 118 B O GLU 129 B O GLU 135 1 A CG HIS 1 A CG HIS 7 1 Y 1 A ND1 HIS 1 A ND1 HIS 7 1 Y 1 A CD2 HIS 1 A CD2 HIS 7 1 Y 1 A CE1 HIS 1 A CE1 HIS 7 1 Y 1 A NE2 HIS 1 A NE2 HIS 7 1 Y 1 A CD LYS 3 A CD LYS 9 1 Y 1 A CE LYS 3 A CE LYS 9 1 Y 1 A NZ LYS 3 A NZ LYS 9 1 Y 1 A CE LYS 18 A CE LYS 24 1 Y 1 A NZ LYS 18 A NZ LYS 24 1 Y 1 A CD1 LEU 28 A CD1 LEU 34 1 Y 1 A CD2 LEU 28 A CD2 LEU 34 1 Y 1 A CD GLN 30 A CD GLN 36 1 Y 1 A OE1 GLN 30 A OE1 GLN 36 1 Y 1 A NE2 GLN 30 A NE2 GLN 36 1 Y 1 A CZ ARG 89 A CZ ARG 95 1 Y 1 A NH1 ARG 89 A NH1 ARG 95 1 Y 1 A NH2 ARG 89 A NH2 ARG 95 1 Y 1 B CG HIS 1 B CG HIS 7 1 Y 1 B ND1 HIS 1 B ND1 HIS 7 1 Y 1 B CD2 HIS 1 B CD2 HIS 7 1 Y 1 B CE1 HIS 1 B CE1 HIS 7 1 Y 1 B NE2 HIS 1 B NE2 HIS 7 1 Y 1 B CD1 LEU 6 B CD1 LEU 12 1 Y 1 B CD2 LEU 6 B CD2 LEU 12 1 Y 1 B CG ASN 17 B CG ASN 23 1 Y 1 B OD1 ASN 17 B OD1 ASN 23 1 Y 1 B ND2 ASN 17 B ND2 ASN 23 1 Y 1 B CG LYS 18 B CG LYS 24 1 Y 1 B CD LYS 18 B CD LYS 24 1 Y 1 B CE LYS 18 B CE LYS 24 1 Y 1 B NZ LYS 18 B NZ LYS 24 1 Y 1 B CG LEU 28 B CG LEU 34 1 Y 1 B CD1 LEU 28 B CD1 LEU 34 1 Y 1 B CD2 LEU 28 B CD2 LEU 34 1 Y 1 B CG GLN 30 B CG GLN 36 1 Y 1 B CD GLN 30 B CD GLN 36 1 Y 1 B OE1 GLN 30 B OE1 GLN 36 1 Y 1 B NE2 GLN 30 B NE2 GLN 36 1 Y 1 B CG LYS 32 B CG LYS 38 1 Y 1 B CD LYS 32 B CD LYS 38 1 Y 1 B CE LYS 32 B CE LYS 38 1 Y 1 B NZ LYS 32 B NZ LYS 38 1 Y 1 B CG ARG 55 B CG ARG 61 1 Y 1 B CD ARG 55 B CD ARG 61 1 Y 1 B NE ARG 55 B NE ARG 61 1 Y 1 B CZ ARG 55 B CZ ARG 61 1 Y 1 B NH1 ARG 55 B NH1 ARG 61 1 Y 1 B NH2 ARG 55 B NH2 ARG 61 1 Y 1 B CG GLU 86 B CG GLU 92 1 Y 1 B CD GLU 86 B CD GLU 92 1 Y 1 B OE1 GLU 86 B OE1 GLU 92 1 Y 1 B OE2 GLU 86 B OE2 GLU 92 1 Y 1 B CD ARG 92 B CD ARG 98 1 Y 1 B NE ARG 92 B NE ARG 98 1 Y 1 B CZ ARG 92 B CZ ARG 98 1 Y 1 B NH1 ARG 92 B NH1 ARG 98 1 Y 1 B NH2 ARG 92 B NH2 ARG 98 1 Y 1 B CG ASN 115 B CG ASN 121 1 Y 1 B OD1 ASN 115 B OD1 ASN 121 1 Y 1 B ND2 ASN 115 B ND2 ASN 121 1 Y 1 B CG ARG 118 B CG ARG 124 1 Y 1 B CD ARG 118 B CD ARG 124 1 Y 1 B NE ARG 118 B NE ARG 124 1 Y 1 B CZ ARG 118 B CZ ARG 124 1 Y 1 B NH1 ARG 118 B NH1 ARG 124 1 Y 1 B NH2 ARG 118 B NH2 ARG 124 1 Y 1 B CG GLU 121 B CG GLU 127 1 Y 1 B CD GLU 121 B CD GLU 127 1 Y 1 B OE1 GLU 121 B OE1 GLU 127 1 Y 1 B OE2 GLU 121 B OE2 GLU 127 1 Y 1 B CZ ARG 122 B CZ ARG 128 1 Y 1 B NH1 ARG 122 B NH1 ARG 128 1 Y 1 B NH2 ARG 122 B NH2 ARG 128 1 Y 1 B CG1 VAL 123 B CG1 VAL 129 1 Y 1 B CG2 VAL 123 B CG2 VAL 129 1 Y 1 A MET -5 A MET 1 1 Y 1 A HIS -4 A HIS 2 1 Y 1 A HIS -3 A HIS 3 1 Y 1 A HIS -2 A HIS 4 1 Y 1 A HIS -1 A HIS 5 1 Y 1 A HIS 0 A HIS 6 1 Y 1 B MET -5 B MET 1 1 Y 1 B HIS -4 B HIS 2 1 Y 1 B HIS -3 B HIS 3 1 Y 1 B HIS -2 B HIS 4 1 Y 1 B HIS -1 B HIS 5 1 Y 1 B HIS 0 B HIS 6 1 Y 1 B PRO 19 B PRO 25 1 Y 1 B ALA 20 B ALA 26 1 Y 1 B SER 21 B SER 27 1 Y 1 B VAL 22 B VAL 28 1 Y 1 B ARG 23 B ARG 29 1 Y 1 B GLU 24 B GLU 30 1 Y 1 B ARG 25 B ARG 31 1 Y 1 B PHE 26 B PHE 32 1 Y 1 B ASN 27 B ASN 33 1 Y 1 A ASN 116 -105.29 -82.90 1 A THR 117 73.90 -22.87 1 B ASN 17 55.17 -119.54 1 B GLN 30 58.81 139.58 0.2259 0.1888 0.1925 1.940 23.44 1925 19319 9.96 92.44 0.29 1 FREE R-VALUE 1.92 MOLECULAR REPLACEMENT 26.21 0.90 1.11 ML FLAT BULK SOLVENT MODEL 1.940 23.44 98 2017 0 0 1919 0.008 1955 1.002 2640 13.306 711 0.046 305 0.005 344 0.6155 0.5954 1.9885 120 1071 79.00 0.2676 0.2356 2.0423 146 1337 100.00 0.2803 0.2196 2.1023 155 1369 100.00 0.2753 0.2021 2.1702 141 1310 100.00 0.2587 0.2168 2.2477 91 806 97.00 0.2705 0.2282 2.3376 91 821 96.00 0.2441 0.2029 2.4439 147 1342 100.00 0.2456 0.2055 2.5727 149 1352 100.00 0.2686 0.1988 2.7337 150 1343 100.00 0.2644 0.2066 2.9444 149 1330 100.00 0.2501 0.2033 3.2402 149 1347 100.00 0.2199 0.1789 3.7078 151 1353 100.00 0.1652 0.1453 4.6666 147 1337 100.00 0.1747 0.1622 25.2874 139 1276 94.00 1.94 23.44 5ECW 1751 1 30.77 6.25 92.4 refinement PHENIX dev_1839 data reduction XDS data scaling XSCALE phasing PHENIX tRNA(fMet)-specific endonuclease VapC (E.C.3.1.-.-) Structure of the Shigella flexneri VapC mutant D7A 1 N N 1 N N 2 N N 2 N N A ALA 7 A ALA 13 HELX_P A ASN 17 A ASN 23 1 AA1 11 A PRO 19 A PRO 25 HELX_P A ASN 29 A ASN 35 1 AA2 11 A SER 37 A SER 43 HELX_P A SER 50 A SER 56 1 AA3 14 A MET 52 A MET 58 HELX_P A SER 65 A SER 71 1 AA4 14 A ASP 73 A ASP 79 HELX_P A GLY 91 A GLY 97 1 AA5 19 A GLY 95 A GLY 101 HELX_P A ARG 108 A ARG 114 1 AA6 14 B ALA 7 B ALA 13 HELX_P B ASN 17 B ASN 23 1 AA7 11 B SER 37 B SER 43 HELX_P B LYS 49 B LYS 55 1 AA8 13 B MET 52 B MET 58 HELX_P B SER 65 B SER 71 1 AA9 14 B ASP 73 B ASP 79 HELX_P B GLY 91 B GLY 97 1 AB1 19 B GLY 95 B GLY 101 HELX_P B ARG 108 B ARG 114 1 AB2 14 B GLU 119 B GLU 125 HELX_P B VAL 123 B VAL 129 5 AB3 5 HYDROLASE Toxin, PIN-domain, hydrolase A LYS 18 A LYS 24 1 A PRO 19 A PRO 25 -7.72 VAPC_SHIFL UNP 1 2 O06662 LKFMLDTNICIFTIKNKPASVRERFNLNQGKMCISSVTLMELIYGAEKSQMPERNLAVIEGFVSRIDVLDYDAAAATHTG QIRAELARQGRPVGPFDQMIAGHARSRGLIIVTNNTREFERVGGLRTEDWS 2 132 5ECW 2 132 O06662 A 1 8 138 2 132 5ECW 2 132 O06662 B 1 8 138 1 initiating methionine MET -5 5ECW A O06662 UNP 1 1 expression tag HIS -4 5ECW A O06662 UNP 2 1 expression tag HIS -3 5ECW A O06662 UNP 3 1 expression tag HIS -2 5ECW A O06662 UNP 4 1 expression tag HIS -1 5ECW A O06662 UNP 5 1 expression tag HIS 0 5ECW A O06662 UNP 6 1 expression tag HIS 1 5ECW A O06662 UNP 7 1 ASP engineered mutation ALA 7 5ECW A O06662 UNP 7 13 2 initiating methionine MET -5 5ECW B O06662 UNP 1 2 expression tag HIS -4 5ECW B O06662 UNP 2 2 expression tag HIS -3 5ECW B O06662 UNP 3 2 expression tag HIS -2 5ECW B O06662 UNP 4 2 expression tag HIS -1 5ECW B O06662 UNP 5 2 expression tag HIS 0 5ECW B O06662 UNP 6 2 expression tag HIS 1 5ECW B O06662 UNP 7 2 ASP engineered mutation ALA 7 5ECW B O06662 UNP 7 13 5 5 parallel parallel parallel parallel parallel parallel parallel parallel A ASP 68 A ASP 74 A LEU 70 A LEU 76 A MET 33 A MET 39 A SER 36 A SER 42 A PHE 4 A PHE 10 A LEU 6 A LEU 12 A ILE 111 A ILE 117 A VAL 113 A VAL 119 A THR 128 A THR 134 A GLU 129 A GLU 135 B ASP 68 B ASP 74 B LEU 70 B LEU 76 B MET 33 B MET 39 B SER 36 B SER 42 B PHE 4 B PHE 10 B LEU 6 B LEU 12 B ILE 111 B ILE 117 B VAL 113 B VAL 119 B THR 128 B THR 134 B GLU 129 B GLU 135 146 H 3