0.026430 -0.008543 -0.000546 0.000000 0.027216 -0.009086 0.000000 0.000000 0.026655 0.000000 0.000000 0.000000 Joint Center for Structural Genomics (JCSG) http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 2 70.350 83.050 72.090 37.836 38.615 39.845 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 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 To be published 0353 Crystal structure of Putative cobalamin (vitamin B12) biosynthesis CbiX protein (YP_958415.1) from Marinobacter aquaeolei VT8 at 1.60 A resolution 10.2210/pdb3lyh/pdb pdb_00003lyh 100 1 Flat collimating mirror, toroid focusing mirror CCD 2010-01-23 MARMOSAIC 325 mm CCD Double crystal monochromator MAD M x-ray 1 0.97915 1.0 0.97903 1.0 0.91162 1.0 BL9-2 SSRL 0.97915,0.97903,0.91162 SYNCHROTRON SSRL BEAMLINE BL9-2 14133.674 Cobalamin (Vitamin B12) biosynthesis CbiX protein 2 man polymer 18.015 water 217 nat water no yes G(MSE)TQPHQIILLAHGSSDARWCETFEKLAEPTVESIENAAIAY(MSE)ELAEPSLDTIVNRAKGQGVEQFTVVPLFL AAGRHLRKDVPA(MSE)IERLEAEHGVTIRLAEPIGKNPRLGLAIRDVVKEELERSEH GMTQPHQIILLAHGSSDARWCETFEKLAEPTVESIENAAIAYMELAEPSLDTIVNRAKGQGVEQFTVVPLFLAAGRHLRK DVPAMIERLEAEHGVTIRLAEPIGKNPRLGLAIRDVVKEELERSEH A,B 403199 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 ATCC 700491 / DSM 11845 / VT8 sample Maqu_1136 351348 Marinobacter aquaeolei 562 Escherichia coli HK100 Plasmid SpeedET 1 1.85 33.34 VAPOR DIFFUSION, SITTING DROP 6.0 20.0000% PEG-6000, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K 277 Joint Center for Structural Genomics JCSG PSI, Protein Structure Initiative software software struct_conn database_2 struct_ref_seq_dif repository Initial release Advisory Version format compliance Refinement description Data collection Derived calculations Refinement description Database references 1 0 2010-04-07 1 1 2011-07-13 1 2 2017-11-08 1 3 2019-07-17 1 4 2023-02-01 _software.classification _software.name _software.classification _software.contact_author _software.contact_author_email _software.language _software.location _software.name _software.type _software.version _struct_conn.pdbx_leaving_atom_flag _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_ref_seq_dif.details Y RCSB Y RCSB 2010-02-26 REL REL HOH water THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. HOH 126 2 HOH HOH 126 A HOH 127 2 HOH HOH 127 A HOH 128 2 HOH HOH 128 A HOH 2 2 HOH HOH 129 A HOH 130 2 HOH HOH 130 A HOH 4 2 HOH HOH 131 A HOH 132 2 HOH HOH 132 A HOH 133 2 HOH HOH 133 A HOH 5 2 HOH HOH 134 A HOH 135 2 HOH HOH 135 A HOH 136 2 HOH HOH 136 A HOH 137 2 HOH HOH 137 A HOH 138 2 HOH HOH 138 A HOH 139 2 HOH HOH 139 A HOH 7 2 HOH HOH 140 A HOH 8 2 HOH HOH 141 A HOH 142 2 HOH HOH 142 A HOH 9 2 HOH HOH 143 A HOH 144 2 HOH HOH 144 A HOH 10 2 HOH HOH 145 A HOH 146 2 HOH HOH 146 A HOH 147 2 HOH HOH 147 A HOH 148 2 HOH HOH 148 A HOH 12 2 HOH HOH 149 A HOH 150 2 HOH HOH 150 A HOH 151 2 HOH HOH 151 A HOH 14 2 HOH HOH 152 A HOH 15 2 HOH HOH 153 A HOH 19 2 HOH HOH 154 A HOH 155 2 HOH HOH 155 A HOH 156 2 HOH HOH 156 A HOH 24 2 HOH HOH 157 A HOH 25 2 HOH HOH 158 A HOH 26 2 HOH HOH 159 A HOH 28 2 HOH HOH 160 A HOH 161 2 HOH HOH 161 A HOH 162 2 HOH HOH 162 A HOH 29 2 HOH HOH 163 A HOH 31 2 HOH HOH 164 A HOH 165 2 HOH HOH 165 A HOH 36 2 HOH HOH 166 A HOH 167 2 HOH HOH 167 A HOH 40 2 HOH HOH 168 A HOH 169 2 HOH HOH 169 A HOH 48 2 HOH HOH 170 A HOH 49 2 HOH HOH 171 A HOH 51 2 HOH HOH 172 A HOH 52 2 HOH HOH 173 A HOH 174 2 HOH HOH 174 A HOH 175 2 HOH HOH 175 A HOH 54 2 HOH HOH 176 A HOH 55 2 HOH HOH 177 A HOH 56 2 HOH HOH 178 A HOH 179 2 HOH HOH 179 A HOH 180 2 HOH HOH 180 A HOH 181 2 HOH HOH 181 A HOH 182 2 HOH HOH 182 A HOH 183 2 HOH HOH 183 A HOH 184 2 HOH HOH 184 A HOH 59 2 HOH HOH 185 A HOH 186 2 HOH HOH 186 A HOH 63 2 HOH HOH 187 A HOH 64 2 HOH HOH 188 A HOH 66 2 HOH HOH 189 A HOH 67 2 HOH HOH 190 A HOH 69 2 HOH HOH 191 A HOH 70 2 HOH HOH 192 A HOH 71 2 HOH HOH 193 A HOH 194 2 HOH HOH 194 A HOH 195 2 HOH HOH 195 A HOH 196 2 HOH HOH 196 A HOH 197 2 HOH HOH 197 A HOH 74 2 HOH HOH 198 A HOH 75 2 HOH HOH 199 A HOH 76 2 HOH HOH 200 A HOH 201 2 HOH HOH 201 A HOH 202 2 HOH HOH 202 A HOH 77 2 HOH HOH 203 A HOH 204 2 HOH HOH 204 A HOH 205 2 HOH HOH 205 A HOH 206 2 HOH HOH 206 A HOH 207 2 HOH HOH 207 A HOH 208 2 HOH HOH 208 A HOH 80 2 HOH HOH 209 A HOH 210 2 HOH HOH 210 A HOH 81 2 HOH HOH 211 A HOH 85 2 HOH HOH 212 A HOH 213 2 HOH HOH 213 A HOH 214 2 HOH HOH 214 A HOH 88 2 HOH HOH 215 A HOH 216 2 HOH HOH 216 A HOH 217 2 HOH HOH 217 A HOH 89 2 HOH HOH 218 A HOH 90 2 HOH HOH 219 A HOH 93 2 HOH HOH 220 A HOH 95 2 HOH HOH 221 A HOH 96 2 HOH HOH 222 A HOH 98 2 HOH HOH 223 A HOH 100 2 HOH HOH 224 A HOH 101 2 HOH HOH 225 A HOH 103 2 HOH HOH 226 A HOH 105 2 HOH HOH 227 A HOH 108 2 HOH HOH 228 A HOH 109 2 HOH HOH 229 A HOH 110 2 HOH HOH 230 A HOH 111 2 HOH HOH 231 A HOH 114 2 HOH HOH 232 A HOH 116 2 HOH HOH 233 A HOH 117 2 HOH HOH 234 A HOH 118 2 HOH HOH 235 A HOH 122 2 HOH HOH 236 A HOH 123 2 HOH HOH 237 A HOH 125 2 HOH HOH 238 A HOH 1 2 HOH HOH 126 B HOH 3 2 HOH HOH 127 B HOH 6 2 HOH HOH 128 B HOH 129 2 HOH HOH 129 B HOH 11 2 HOH HOH 130 B HOH 131 2 HOH HOH 131 B HOH 13 2 HOH HOH 132 B HOH 16 2 HOH HOH 133 B HOH 134 2 HOH HOH 134 B HOH 17 2 HOH HOH 135 B HOH 18 2 HOH HOH 136 B HOH 20 2 HOH HOH 137 B HOH 21 2 HOH HOH 138 B HOH 22 2 HOH HOH 139 B HOH 140 2 HOH HOH 140 B HOH 141 2 HOH HOH 141 B HOH 23 2 HOH HOH 142 B HOH 143 2 HOH HOH 143 B HOH 27 2 HOH HOH 144 B HOH 145 2 HOH HOH 145 B HOH 30 2 HOH HOH 146 B HOH 32 2 HOH HOH 147 B HOH 33 2 HOH HOH 148 B HOH 149 2 HOH HOH 149 B HOH 34 2 HOH HOH 150 B HOH 35 2 HOH HOH 151 B HOH 152 2 HOH HOH 152 B HOH 153 2 HOH HOH 153 B HOH 154 2 HOH HOH 154 B HOH 37 2 HOH HOH 155 B HOH 38 2 HOH HOH 156 B HOH 157 2 HOH HOH 157 B HOH 158 2 HOH HOH 158 B HOH 159 2 HOH HOH 159 B HOH 160 2 HOH HOH 160 B HOH 39 2 HOH HOH 161 B HOH 41 2 HOH HOH 162 B HOH 163 2 HOH HOH 163 B HOH 164 2 HOH HOH 164 B HOH 42 2 HOH HOH 165 B HOH 166 2 HOH HOH 166 B HOH 43 2 HOH HOH 167 B HOH 168 2 HOH HOH 168 B HOH 44 2 HOH HOH 169 B HOH 170 2 HOH HOH 170 B HOH 171 2 HOH HOH 171 B HOH 172 2 HOH HOH 172 B HOH 173 2 HOH HOH 173 B HOH 45 2 HOH HOH 174 B HOH 46 2 HOH HOH 175 B HOH 176 2 HOH HOH 176 B HOH 177 2 HOH HOH 177 B HOH 178 2 HOH HOH 178 B HOH 47 2 HOH HOH 179 B HOH 50 2 HOH HOH 180 B HOH 53 2 HOH HOH 181 B HOH 57 2 HOH HOH 182 B HOH 58 2 HOH HOH 183 B HOH 60 2 HOH HOH 184 B HOH 185 2 HOH HOH 185 B HOH 61 2 HOH HOH 186 B HOH 187 2 HOH HOH 187 B HOH 188 2 HOH HOH 188 B HOH 189 2 HOH HOH 189 B HOH 190 2 HOH HOH 190 B HOH 191 2 HOH HOH 191 B HOH 192 2 HOH HOH 192 B HOH 193 2 HOH HOH 193 B HOH 62 2 HOH HOH 194 B HOH 65 2 HOH HOH 195 B HOH 68 2 HOH HOH 196 B HOH 72 2 HOH HOH 197 B HOH 198 2 HOH HOH 198 B HOH 199 2 HOH HOH 199 B HOH 200 2 HOH HOH 200 B HOH 73 2 HOH HOH 201 B HOH 78 2 HOH HOH 202 B HOH 203 2 HOH HOH 203 B HOH 79 2 HOH HOH 204 B HOH 82 2 HOH HOH 205 B HOH 83 2 HOH HOH 206 B HOH 84 2 HOH HOH 207 B HOH 86 2 HOH HOH 208 B HOH 209 2 HOH HOH 209 B HOH 87 2 HOH HOH 210 B HOH 211 2 HOH HOH 211 B HOH 212 2 HOH HOH 212 B HOH 91 2 HOH HOH 213 B HOH 92 2 HOH HOH 214 B HOH 215 2 HOH HOH 215 B HOH 94 2 HOH HOH 216 B HOH 97 2 HOH HOH 217 B HOH 99 2 HOH HOH 218 B HOH 102 2 HOH HOH 219 B HOH 104 2 HOH HOH 220 B HOH 106 2 HOH HOH 221 B HOH 107 2 HOH HOH 222 B HOH 112 2 HOH HOH 223 B HOH 113 2 HOH HOH 224 B HOH 115 2 HOH HOH 225 B HOH 119 2 HOH HOH 226 B HOH 120 2 HOH HOH 227 B HOH 121 2 HOH HOH 228 B HOH 124 2 HOH HOH 229 B n 1 0 A n 2 1 A n 3 2 A n 4 3 A PRO 4 n 5 PRO 4 A HIS 5 n 6 HIS 5 A GLN 6 n 7 GLN 6 A ILE 7 n 8 ILE 7 A ILE 8 n 9 ILE 8 A LEU 9 n 10 LEU 9 A LEU 10 n 11 LEU 10 A ALA 11 n 12 ALA 11 A HIS 12 n 13 HIS 12 A GLY 13 n 14 GLY 13 A SER 14 n 15 SER 14 A SER 15 n 16 SER 15 A ASP 16 n 17 ASP 16 A ALA 17 n 18 ALA 17 A ARG 18 n 19 ARG 18 A TRP 19 n 20 TRP 19 A CYS 20 n 21 CYS 20 A GLU 21 n 22 GLU 21 A THR 22 n 23 THR 22 A PHE 23 n 24 PHE 23 A GLU 24 n 25 GLU 24 A LYS 25 n 26 LYS 25 A LEU 26 n 27 LEU 26 A ALA 27 n 28 ALA 27 A GLU 28 n 29 GLU 28 A PRO 29 n 30 PRO 29 A THR 30 n 31 THR 30 A VAL 31 n 32 VAL 31 A GLU 32 n 33 GLU 32 A SER 33 n 34 SER 33 A ILE 34 n 35 ILE 34 A GLU 35 n 36 GLU 35 A ASN 36 n 37 ASN 36 A ALA 37 n 38 ALA 37 A ALA 38 n 39 ALA 38 A ILE 39 n 40 ILE 39 A ALA 40 n 41 ALA 40 A TYR 41 n 42 TYR 41 A MSE 42 n 43 MSE 42 A GLU 43 n 44 GLU 43 A LEU 44 n 45 LEU 44 A ALA 45 n 46 ALA 45 A GLU 46 n 47 GLU 46 A PRO 47 n 48 PRO 47 A SER 48 n 49 SER 48 A LEU 49 n 50 LEU 49 A ASP 50 n 51 ASP 50 A THR 51 n 52 THR 51 A ILE 52 n 53 ILE 52 A VAL 53 n 54 VAL 53 A ASN 54 n 55 ASN 54 A ARG 55 n 56 ARG 55 A ALA 56 n 57 ALA 56 A LYS 57 n 58 LYS 57 A GLY 58 n 59 GLY 58 A GLN 59 n 60 GLN 59 A GLY 60 n 61 GLY 60 A VAL 61 n 62 VAL 61 A GLU 62 n 63 GLU 62 A GLN 63 n 64 GLN 63 A PHE 64 n 65 PHE 64 A THR 65 n 66 THR 65 A VAL 66 n 67 VAL 66 A VAL 67 n 68 VAL 67 A PRO 68 n 69 PRO 68 A LEU 69 n 70 LEU 69 A PHE 70 n 71 PHE 70 A LEU 71 n 72 LEU 71 A ALA 72 n 73 ALA 72 A ALA 73 n 74 ALA 73 A GLY 74 n 75 GLY 74 A ARG 75 n 76 ARG 75 A HIS 76 n 77 HIS 76 A LEU 77 n 78 LEU 77 A ARG 78 n 79 ARG 78 A LYS 79 n 80 LYS 79 A ASP 80 n 81 ASP 80 A VAL 81 n 82 VAL 81 A PRO 82 n 83 PRO 82 A ALA 83 n 84 ALA 83 A MSE 84 n 85 MSE 84 A ILE 85 n 86 ILE 85 A GLU 86 n 87 GLU 86 A ARG 87 n 88 ARG 87 A LEU 88 n 89 LEU 88 A GLU 89 n 90 GLU 89 A ALA 90 n 91 ALA 90 A GLU 91 n 92 GLU 91 A HIS 92 n 93 HIS 92 A GLY 93 n 94 GLY 93 A VAL 94 n 95 VAL 94 A THR 95 n 96 THR 95 A ILE 96 n 97 ILE 96 A ARG 97 n 98 ARG 97 A LEU 98 n 99 LEU 98 A ALA 99 n 100 ALA 99 A GLU 100 n 101 GLU 100 A PRO 101 n 102 PRO 101 A ILE 102 n 103 ILE 102 A GLY 103 n 104 GLY 103 A LYS 104 n 105 LYS 104 A ASN 105 n 106 ASN 105 A PRO 106 n 107 PRO 106 A ARG 107 n 108 ARG 107 A LEU 108 n 109 LEU 108 A GLY 109 n 110 GLY 109 A LEU 110 n 111 LEU 110 A ALA 111 n 112 ALA 111 A ILE 112 n 113 ILE 112 A ARG 113 n 114 ARG 113 A ASP 114 n 115 ASP 114 A VAL 115 n 116 VAL 115 A VAL 116 n 117 VAL 116 A LYS 117 n 118 LYS 117 A GLU 118 n 119 GLU 118 A GLU 119 n 120 GLU 119 A LEU 120 n 121 LEU 120 A GLU 121 n 122 GLU 121 A ARG 122 n 123 ARG 122 A SER 123 n 124 SER 123 A n 125 124 A n 126 125 A n 1 0 B n 2 1 B n 3 2 B GLN 3 n 4 GLN 3 B PRO 4 n 5 PRO 4 B HIS 5 n 6 HIS 5 B GLN 6 n 7 GLN 6 B ILE 7 n 8 ILE 7 B ILE 8 n 9 ILE 8 B LEU 9 n 10 LEU 9 B LEU 10 n 11 LEU 10 B ALA 11 n 12 ALA 11 B HIS 12 n 13 HIS 12 B GLY 13 n 14 GLY 13 B SER 14 n 15 SER 14 B SER 15 n 16 SER 15 B ASP 16 n 17 ASP 16 B ALA 17 n 18 ALA 17 B ARG 18 n 19 ARG 18 B TRP 19 n 20 TRP 19 B CYS 20 n 21 CYS 20 B GLU 21 n 22 GLU 21 B THR 22 n 23 THR 22 B PHE 23 n 24 PHE 23 B GLU 24 n 25 GLU 24 B LYS 25 n 26 LYS 25 B LEU 26 n 27 LEU 26 B ALA 27 n 28 ALA 27 B GLU 28 n 29 GLU 28 B PRO 29 n 30 PRO 29 B THR 30 n 31 THR 30 B VAL 31 n 32 VAL 31 B GLU 32 n 33 GLU 32 B SER 33 n 34 SER 33 B ILE 34 n 35 ILE 34 B GLU 35 n 36 GLU 35 B ASN 36 n 37 ASN 36 B ALA 37 n 38 ALA 37 B ALA 38 n 39 ALA 38 B ILE 39 n 40 ILE 39 B ALA 40 n 41 ALA 40 B TYR 41 n 42 TYR 41 B MSE 42 n 43 MSE 42 B GLU 43 n 44 GLU 43 B LEU 44 n 45 LEU 44 B ALA 45 n 46 ALA 45 B GLU 46 n 47 GLU 46 B PRO 47 n 48 PRO 47 B SER 48 n 49 SER 48 B LEU 49 n 50 LEU 49 B ASP 50 n 51 ASP 50 B THR 51 n 52 THR 51 B ILE 52 n 53 ILE 52 B VAL 53 n 54 VAL 53 B ASN 54 n 55 ASN 54 B ARG 55 n 56 ARG 55 B ALA 56 n 57 ALA 56 B LYS 57 n 58 LYS 57 B GLY 58 n 59 GLY 58 B GLN 59 n 60 GLN 59 B GLY 60 n 61 GLY 60 B VAL 61 n 62 VAL 61 B GLU 62 n 63 GLU 62 B GLN 63 n 64 GLN 63 B PHE 64 n 65 PHE 64 B THR 65 n 66 THR 65 B VAL 66 n 67 VAL 66 B VAL 67 n 68 VAL 67 B PRO 68 n 69 PRO 68 B LEU 69 n 70 LEU 69 B PHE 70 n 71 PHE 70 B LEU 71 n 72 LEU 71 B ALA 72 n 73 ALA 72 B ALA 73 n 74 ALA 73 B GLY 74 n 75 GLY 74 B n 76 75 B HIS 76 n 77 HIS 76 B LEU 77 n 78 LEU 77 B ARG 78 n 79 ARG 78 B LYS 79 n 80 LYS 79 B ASP 80 n 81 ASP 80 B VAL 81 n 82 VAL 81 B PRO 82 n 83 PRO 82 B ALA 83 n 84 ALA 83 B MSE 84 n 85 MSE 84 B ILE 85 n 86 ILE 85 B GLU 86 n 87 GLU 86 B ARG 87 n 88 ARG 87 B LEU 88 n 89 LEU 88 B GLU 89 n 90 GLU 89 B ALA 90 n 91 ALA 90 B GLU 91 n 92 GLU 91 B HIS 92 n 93 HIS 92 B GLY 93 n 94 GLY 93 B VAL 94 n 95 VAL 94 B THR 95 n 96 THR 95 B ILE 96 n 97 ILE 96 B ARG 97 n 98 ARG 97 B LEU 98 n 99 LEU 98 B ALA 99 n 100 ALA 99 B GLU 100 n 101 GLU 100 B PRO 101 n 102 PRO 101 B ILE 102 n 103 ILE 102 B GLY 103 n 104 GLY 103 B LYS 104 n 105 LYS 104 B ASN 105 n 106 ASN 105 B PRO 106 n 107 PRO 106 B ARG 107 n 108 ARG 107 B LEU 108 n 109 LEU 108 B GLY 109 n 110 GLY 109 B LEU 110 n 111 LEU 110 B ALA 111 n 112 ALA 111 B ILE 112 n 113 ILE 112 B ARG 113 n 114 ARG 113 B ASP 114 n 115 ASP 114 B VAL 115 n 116 VAL 115 B VAL 116 n 117 VAL 116 B LYS 117 n 118 LYS 117 B GLU 118 n 119 GLU 118 B GLU 119 n 120 GLU 119 B LEU 120 n 121 LEU 120 B GLU 121 n 122 GLU 121 B ARG 122 n 123 ARG 122 B SER 123 n 124 SER 123 B GLU 124 n 125 GLU 124 B HIS 125 n 126 HIS 125 B 0.5134 -0.0765 -0.0744 0.6021 0.5339 1.3116 0.0552 0.0504 -0.0094 0.0255 -0.0138 -0.0205 0.0567 0.0637 -0.0414 0.0133 0.0097 0.0024 0.0150 0.0025 0.0141 refined 43.7798 33.6772 7.6424 X-RAY DIFFRACTION 0.6571 0.1883 0.2532 0.5340 0.6019 1.0500 -0.0482 -0.0020 0.0908 0.0107 -0.0246 0.0282 -0.0381 -0.0396 0.0728 0.0172 -0.0009 -0.0051 0.0121 0.0056 0.0282 refined 34.0782 48.4636 19.2297 X-RAY DIFFRACTION A 4 A 123 X-RAY DIFFRACTION 1 B 3 B 125 X-RAY DIFFRACTION 2 author_and_software_defined_assembly PISA 2 dimeric 4150 -30 11340 A MSE 42 SELENOMETHIONINE A MSE 43 MET A MSE 84 SELENOMETHIONINE A MSE 85 MET B MSE 42 SELENOMETHIONINE B MSE 43 MET B MSE 84 SELENOMETHIONINE B MSE 85 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 A O ALA 40 A O ALA 41 A N ALA 11 A N ALA 12 A N ILE 8 A N ILE 9 A O VAL 67 A O VAL 68 A N VAL 66 A N VAL 67 A O ARG 97 A O ARG 98 B O ALA 38 B O ALA 39 B N LEU 9 B N LEU 10 B N ILE 8 B N ILE 9 B O VAL 67 B O VAL 68 B N VAL 66 B N VAL 67 B O ARG 97 B O ARG 98 1 A CG PRO 4 A CG PRO 5 1 Y 1 A CD PRO 4 A CD PRO 5 1 Y 1 A CG GLU 35 A CG GLU 36 1 Y 1 A CD GLU 35 A CD GLU 36 1 Y 1 A OE1 GLU 35 A OE1 GLU 36 1 Y 1 A OE2 GLU 35 A OE2 GLU 36 1 Y 1 A CD ARG 75 A CD ARG 76 1 Y 1 A NE ARG 75 A NE ARG 76 1 Y 1 A CZ ARG 75 A CZ ARG 76 1 Y 1 A NH1 ARG 75 A NH1 ARG 76 1 Y 1 A NH2 ARG 75 A NH2 ARG 76 1 Y 1 A CG GLU 121 A CG GLU 122 1 Y 1 A CD GLU 121 A CD GLU 122 1 Y 1 A OE1 GLU 121 A OE1 GLU 122 1 Y 1 A OE2 GLU 121 A OE2 GLU 122 1 Y 1 A CG ARG 122 A CG ARG 123 1 Y 1 A CD ARG 122 A CD ARG 123 1 Y 1 A NE ARG 122 A NE ARG 123 1 Y 1 A CZ ARG 122 A CZ ARG 123 1 Y 1 A NH1 ARG 122 A NH1 ARG 123 1 Y 1 A NH2 ARG 122 A NH2 ARG 123 1 Y 1 B CG GLN 3 B CG GLN 4 1 Y 1 B CD GLN 3 B CD GLN 4 1 Y 1 B OE1 GLN 3 B OE1 GLN 4 1 Y 1 B NE2 GLN 3 B NE2 GLN 4 1 Y 1 B CD ARG 18 B CD ARG 19 1 Y 1 B NE ARG 18 B NE ARG 19 1 Y 1 B CZ ARG 18 B CZ ARG 19 1 Y 1 B NH1 ARG 18 B NH1 ARG 19 1 Y 1 B NH2 ARG 18 B NH2 ARG 19 1 Y 1 B CD LYS 25 B CD LYS 26 1 Y 1 B CE LYS 25 B CE LYS 26 1 Y 1 B NZ LYS 25 B NZ LYS 26 1 Y 1 B CG HIS 76 B CG HIS 77 1 Y 1 B ND1 HIS 76 B ND1 HIS 77 1 Y 1 B CD2 HIS 76 B CD2 HIS 77 1 Y 1 B CE1 HIS 76 B CE1 HIS 77 1 Y 1 B NE2 HIS 76 B NE2 HIS 77 1 Y 1 B CG LEU 77 B CG LEU 78 1 Y 1 B CD1 LEU 77 B CD1 LEU 78 1 Y 1 B CD2 LEU 77 B CD2 LEU 78 1 Y 1 B CD LYS 79 B CD LYS 80 1 Y 1 B CE LYS 79 B CE LYS 80 1 Y 1 B NZ LYS 79 B NZ LYS 80 1 Y 1 B CG HIS 125 B CG HIS 126 1 Y 1 B ND1 HIS 125 B ND1 HIS 126 1 Y 1 B CD2 HIS 125 B CD2 HIS 126 1 Y 1 B CE1 HIS 125 B CE1 HIS 126 1 Y 1 B NE2 HIS 125 B NE2 HIS 126 1 Y 1 A GLY 0 A GLY 1 1 Y 1 A MSE 1 A MSE 2 1 Y 1 A THR 2 A THR 3 1 Y 1 A GLN 3 A GLN 4 1 Y 1 A GLU 124 A GLU 125 1 Y 1 A HIS 125 A HIS 126 1 Y 1 B GLY 0 B GLY 1 1 Y 1 B MSE 1 B MSE 2 1 Y 1 B THR 2 B THR 3 1 Y 1 B ARG 75 B ARG 76 1 Y 1 3.08 0.50 120.30 123.38 B B B NE CZ NH1 ARG ARG ARG 78 78 78 N 1 A LEU 44 73.10 -24.93 1 B LEU 44 63.36 -11.73 60.53 19.754 2.43 0.070 -1.080 1.110 1.130 -1.160 -0.020 0.966 0.952 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 0.209 0.170 0.172 1.600 29.618 1291 25860 5.000 96.460 1.00 0.30 4.121 0.065 RANDOM LIKELY RESIDUAL 1 THROUGHOUT 0.00 MAD 0.103 0.102 0.800 0.800 1.200 MAXIMUM LIKELIHOOD WITH PHASES MASK 1.600 29.618 217 2054 0 0 1837 0.016 0.022 1983 0.002 0.020 1339 1.645 1.977 2716 1.151 3.000 3303 6.166 5.000 272 36.175 24.419 86 13.339 15.000 348 16.660 15.000 14 0.097 0.200 319 0.007 0.021 2237 0.001 0.020 374 1.918 3.000 1262 0.527 3.000 503 3.135 5.000 2044 5.390 8.000 721 8.550 11.000 657 0.231 0.252 1.639 77 1729 1806 20 91.580 1.60 29.618 3LYH 25860 0.054 1 3.300 96.700 refinement Garib N. Murshudov garib@ysbl.york.ac.uk Fortran_77 http://www.ccp4.ac.uk/dist/html/refmac5.html REFMAC program 5.5.0102 refinement P.D. Adams PDAdams@lbl.gov C++ http://www.phenix-online.org/ PHENIX package phasing George M. Sheldrick gsheldr@shelx.uni-ac.gwdg.de Fortran_77 http://shelx.uni-ac.gwdg.de/SHELX/ SHELX package model building D.C. & J.S. Richardson lab molprobity@kinemage.biochem.duke.edu http://kinemage.biochem.duke.edu/molprobity/ MolProbity package 3beta29 data scaling Phil R. Evans pre@mrc-lmb.cam.ac.uk 2009/03/31 Fortran_77 http://www.ccp4.ac.uk/dist/html/scala.html SCALA other 3.3.15 data extraction PDB help@deposit.rcsb.org June 11, 2008 C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ PDB_EXTRACT package 3.006 data reduction MOSFLM phasing SHELXD phasing autoSHARP Crystal structure of Putative cobalamin (vitamin B12) biosynthesis CbiX protein (YP_958415.1) from Marinobacter aquaeolei VT8 at 1.60 A resolution 1 N N 1 N N 2 N N 2 N N A ASP 16 A ASP 17 HELX_P A ILE 34 A ILE 35 1 1 19 A SER 48 A SER 49 HELX_P A GLN 59 A GLN 60 1 2 12 A GLY 74 A GLY 75 HELX_P A GLY 93 A GLY 94 1 3 20 A PRO 101 A PRO 102 HELX_P A LYS 104 A LYS 105 5 4 4 A ASN 105 A ASN 106 HELX_P A SER 123 A SER 124 1 5 19 B ASP 16 B ASP 17 HELX_P B ILE 34 B ILE 35 1 6 19 B SER 48 B SER 49 HELX_P B GLN 59 B GLN 60 1 7 12 B HIS 76 B HIS 77 HELX_P B GLY 93 B GLY 94 1 8 18 B PRO 101 B PRO 102 HELX_P B LYS 104 B LYS 105 5 9 4 B ASN 105 B ASN 106 HELX_P B HIS 125 B HIS 126 1 10 21 covale 1.330 both A TYR 41 A C TYR 42 1_555 A MSE 42 A N MSE 43 1_555 covale 1.328 both A MSE 42 A C MSE 43 1_555 A GLU 43 A N GLU 44 1_555 covale 1.334 both A ALA 83 A C ALA 84 1_555 A MSE 84 A N MSE 85 1_555 covale 1.334 both A MSE 84 A C MSE 85 1_555 A ILE 85 A N ILE 86 1_555 covale 1.317 both B TYR 41 B C TYR 42 1_555 B MSE 42 B N MSE 43 1_555 covale 1.338 both B MSE 42 B C MSE 43 1_555 B GLU 43 B N GLU 44 1_555 covale 1.333 both B ALA 83 B C ALA 84 1_555 B MSE 84 B N MSE 85 1_555 covale 1.339 both B MSE 84 B C MSE 85 1_555 B ILE 85 B N ILE 86 1_555 LYASE Putative cobalamin (vitamin B12) biosynthesis CbiX protein, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, LYASE A GLU 46 A GLU 47 1 A PRO 47 A PRO 48 -0.32 B GLN 3 B GLN 4 1 B PRO 4 B PRO 5 -22.75 B GLU 46 B GLU 47 1 B PRO 47 B PRO 48 2.63 A1TZQ9_MARAV UNP 1 1 A1TZQ9 MTQPHQIILLAHGSSDARWCETFEKLAEPTVESIENAAIAYMELAEPSLDTIVNRAKGQGVEQFTVVPLFLAAGRHLRKD VPAMIERLEAEHGVTIRLAEPIGKNPRLGLAIRDVVKEELERSEH 1 125 3LYH 1 125 A1TZQ9 A 1 2 126 1 125 3LYH 1 125 A1TZQ9 B 1 2 126 1 expression tag GLY 0 3LYH A A1TZQ9 UNP 1 2 expression tag GLY 0 3LYH B A1TZQ9 UNP 1 4 4 parallel parallel parallel parallel parallel parallel A ALA 38 A ALA 39 A TYR 41 A TYR 42 A HIS 5 A HIS 6 A ALA 11 A ALA 12 A GLN 63 A GLN 64 A PRO 68 A PRO 69 A THR 95 A THR 96 A LEU 98 A LEU 99 B ALA 37 B ALA 38 B TYR 41 B TYR 42 B HIS 5 B HIS 6 B ALA 11 B ALA 12 B GLN 63 B GLN 64 B PRO 68 B PRO 69 B THR 95 B THR 96 B LEU 98 B LEU 99 1 P 1