0.006156 0.000000 0.000000 0.000000 0.006156 0.000000 0.000000 0.000000 0.006156 0.000000 0.000000 0.000000 Joint Center for Structural Genomics (JCSG) http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 48 90.000 90.000 90.000 162.440 162.440 162.440 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 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 O4 S -2 96.063 SULFATE ION non-polymer 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 a Putative DNA replication regulator Hda (Sama_1916) from SHEWANELLA AMAZONENSIS SB2B at 3.00 A resolution 10.2210/pdb3sc3/pdb pdb_00003sc3 100 1 Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing) CCD 2008-11-15 MARMOSAIC 325 mm CCD single crystal Si(111) bent SINGLE WAVELENGTH M x-ray 1 0.97799 1.0 BL11-1 SSRL 0.97799 SYNCHROTRON SSRL BEAMLINE BL11-1 25509.047 Putative DNA replication regulator Hda 2 man polymer 96.063 SULFATE ION 5 syn non-polymer Regulatory inactivation of DnaA Hda protein no yes GVHLPDDETFTSYYPAAGNDELIGALKSAASGDGVQAIYLWGPVKSGRTHLIHAACARANELERRSFYIPLGIHASISTA LLEGLEQFDLICIDDVDAVAGHPLWEEAIFDLYNRVAEQKRGSLIVSASASP(MSE)EAGFVLPDLVSR(MSE)HWGLTY QLQP(MSE)(MSE)DDEKLAALQRRAA(MSE)RGLQLPEDVGRFLLNR(MSE)ARDLRTLFDVLDRLDKAS(MSE)VHQR KLTIPFVKE(MSE)LRL GVHLPDDETFTSYYPAAGNDELIGALKSAASGDGVQAIYLWGPVKSGRTHLIHAACARANELERRSFYIPLGIHASISTA LLEGLEQFDLICIDDVDAVAGHPLWEEAIFDLYNRVAEQKRGSLIVSASASPMEAGFVLPDLVSRMHWGLTYQLQPMMDD EKLAALQRRAAMRGLQLPEDVGRFLLNRMARDLRTLFDVLDRLDKASMVHQRKLTIPFVKEMLRL A,B 396931 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 n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n SB2B sample SAMA_14OCT04_CONTIG53_REVISED_GENE1514, Sama_1916 326297 Shewanella amazonensis 562 Escherichia Coli HK100 Plasmid SpeedET 1 3.50 64.86 VAPOR DIFFUSION, SITTING DROP 7.5 1.26M (NH4)2SO4, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K 277 Joint Center for Structural Genomics JCSG PSI:Biology pdbx_struct_assembly_auth_evidence software citation_author database_2 struct_conn struct_ref_seq_dif struct_site repository Initial release Author supporting evidence Refinement description Database references Database references Derived calculations 1 0 2011-07-13 1 1 2017-10-25 1 2 2018-01-24 1 3 2023-02-01 _citation_author.name _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Crystal structure of a putative DNA replication regulator Hda (Sama_1916) from Shewanella amazonensis SB2B at 1.75 A resolution - CDP and Mg2+ bound Y RCSB Y RCSB 2011-06-06 REL REL SO4 SULFATE ION THE CONSTRUCT (RESIDUES 18-241) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. SO4 1 2 SO4 SO4 1 A SO4 2 2 SO4 SO4 2 A SO4 3 2 SO4 SO4 3 B SO4 4 2 SO4 SO4 4 B SO4 5 2 SO4 SO4 5 B n 1 0 A n 2 18 A n 3 19 A n 4 20 A n 5 21 A n 6 22 A n 7 23 A n 8 24 A n 9 25 A n 10 26 A n 11 27 A n 12 28 A n 13 29 A TYR 30 n 14 TYR 30 A PRO 31 n 15 PRO 31 A ALA 32 n 16 ALA 32 A ALA 33 n 17 ALA 33 A GLY 34 n 18 GLY 34 A ASN 35 n 19 ASN 35 A ASP 36 n 20 ASP 36 A GLU 37 n 21 GLU 37 A LEU 38 n 22 LEU 38 A ILE 39 n 23 ILE 39 A GLY 40 n 24 GLY 40 A ALA 41 n 25 ALA 41 A LEU 42 n 26 LEU 42 A LYS 43 n 27 LYS 43 A SER 44 n 28 SER 44 A ALA 45 n 29 ALA 45 A ALA 46 n 30 ALA 46 A SER 47 n 31 SER 47 A GLY 48 n 32 GLY 48 A ASP 49 n 33 ASP 49 A GLY 50 n 34 GLY 50 A VAL 51 n 35 VAL 51 A GLN 52 n 36 GLN 52 A ALA 53 n 37 ALA 53 A ILE 54 n 38 ILE 54 A TYR 55 n 39 TYR 55 A LEU 56 n 40 LEU 56 A TRP 57 n 41 TRP 57 A GLY 58 n 42 GLY 58 A PRO 59 n 43 PRO 59 A VAL 60 n 44 VAL 60 A LYS 61 n 45 LYS 61 A SER 62 n 46 SER 62 A GLY 63 n 47 GLY 63 A ARG 64 n 48 ARG 64 A THR 65 n 49 THR 65 A HIS 66 n 50 HIS 66 A LEU 67 n 51 LEU 67 A ILE 68 n 52 ILE 68 A HIS 69 n 53 HIS 69 A ALA 70 n 54 ALA 70 A ALA 71 n 55 ALA 71 A CYS 72 n 56 CYS 72 A ALA 73 n 57 ALA 73 A ARG 74 n 58 ARG 74 A ALA 75 n 59 ALA 75 A ASN 76 n 60 ASN 76 A GLU 77 n 61 GLU 77 A LEU 78 n 62 LEU 78 A GLU 79 n 63 GLU 79 A ARG 80 n 64 ARG 80 A ARG 81 n 65 ARG 81 A SER 82 n 66 SER 82 A PHE 83 n 67 PHE 83 A TYR 84 n 68 TYR 84 A ILE 85 n 69 ILE 85 A PRO 86 n 70 PRO 86 A LEU 87 n 71 LEU 87 A GLY 88 n 72 GLY 88 A ILE 89 n 73 ILE 89 A HIS 90 n 74 HIS 90 A ALA 91 n 75 ALA 91 A SER 92 n 76 SER 92 A ILE 93 n 77 ILE 93 A SER 94 n 78 SER 94 A THR 95 n 79 THR 95 A ALA 96 n 80 ALA 96 A LEU 97 n 81 LEU 97 A LEU 98 n 82 LEU 98 A GLU 99 n 83 GLU 99 A GLY 100 n 84 GLY 100 A LEU 101 n 85 LEU 101 A GLU 102 n 86 GLU 102 A GLN 103 n 87 GLN 103 A PHE 104 n 88 PHE 104 A ASP 105 n 89 ASP 105 A LEU 106 n 90 LEU 106 A ILE 107 n 91 ILE 107 A CYS 108 n 92 CYS 108 A ILE 109 n 93 ILE 109 A ASP 110 n 94 ASP 110 A ASP 111 n 95 ASP 111 A VAL 112 n 96 VAL 112 A ASP 113 n 97 ASP 113 A ALA 114 n 98 ALA 114 A VAL 115 n 99 VAL 115 A ALA 116 n 100 ALA 116 A GLY 117 n 101 GLY 117 A HIS 118 n 102 HIS 118 A PRO 119 n 103 PRO 119 A LEU 120 n 104 LEU 120 A TRP 121 n 105 TRP 121 A GLU 122 n 106 GLU 122 A GLU 123 n 107 GLU 123 A ALA 124 n 108 ALA 124 A ILE 125 n 109 ILE 125 A PHE 126 n 110 PHE 126 A ASP 127 n 111 ASP 127 A LEU 128 n 112 LEU 128 A TYR 129 n 113 TYR 129 A ASN 130 n 114 ASN 130 A ARG 131 n 115 ARG 131 A VAL 132 n 116 VAL 132 A ALA 133 n 117 ALA 133 A GLU 134 n 118 GLU 134 A GLN 135 n 119 GLN 135 A LYS 136 n 120 LYS 136 A ARG 137 n 121 ARG 137 A GLY 138 n 122 GLY 138 A SER 139 n 123 SER 139 A LEU 140 n 124 LEU 140 A ILE 141 n 125 ILE 141 A VAL 142 n 126 VAL 142 A SER 143 n 127 SER 143 A ALA 144 n 128 ALA 144 A SER 145 n 129 SER 145 A ALA 146 n 130 ALA 146 A SER 147 n 131 SER 147 A PRO 148 n 132 PRO 148 A MSE 149 n 133 MSE 149 A GLU 150 n 134 GLU 150 A ALA 151 n 135 ALA 151 A GLY 152 n 136 GLY 152 A PHE 153 n 137 PHE 153 A VAL 154 n 138 VAL 154 A LEU 155 n 139 LEU 155 A PRO 156 n 140 PRO 156 A ASP 157 n 141 ASP 157 A LEU 158 n 142 LEU 158 A VAL 159 n 143 VAL 159 A SER 160 n 144 SER 160 A ARG 161 n 145 ARG 161 A MSE 162 n 146 MSE 162 A HIS 163 n 147 HIS 163 A TRP 164 n 148 TRP 164 A GLY 165 n 149 GLY 165 A LEU 166 n 150 LEU 166 A THR 167 n 151 THR 167 A TYR 168 n 152 TYR 168 A GLN 169 n 153 GLN 169 A LEU 170 n 154 LEU 170 A GLN 171 n 155 GLN 171 A PRO 172 n 156 PRO 172 A MSE 173 n 157 MSE 173 A MSE 174 n 158 MSE 174 A ASP 175 n 159 ASP 175 A ASP 176 n 160 ASP 176 A GLU 177 n 161 GLU 177 A LYS 178 n 162 LYS 178 A LEU 179 n 163 LEU 179 A ALA 180 n 164 ALA 180 A ALA 181 n 165 ALA 181 A LEU 182 n 166 LEU 182 A GLN 183 n 167 GLN 183 A ARG 184 n 168 ARG 184 A ARG 185 n 169 ARG 185 A ALA 186 n 170 ALA 186 A ALA 187 n 171 ALA 187 A MSE 188 n 172 MSE 188 A ARG 189 n 173 ARG 189 A GLY 190 n 174 GLY 190 A LEU 191 n 175 LEU 191 A GLN 192 n 176 GLN 192 A LEU 193 n 177 LEU 193 A PRO 194 n 178 PRO 194 A GLU 195 n 179 GLU 195 A ASP 196 n 180 ASP 196 A VAL 197 n 181 VAL 197 A GLY 198 n 182 GLY 198 A ARG 199 n 183 ARG 199 A PHE 200 n 184 PHE 200 A LEU 201 n 185 LEU 201 A LEU 202 n 186 LEU 202 A ASN 203 n 187 ASN 203 A ARG 204 n 188 ARG 204 A MSE 205 n 189 MSE 205 A ALA 206 n 190 ALA 206 A ARG 207 n 191 ARG 207 A ASP 208 n 192 ASP 208 A LEU 209 n 193 LEU 209 A ARG 210 n 194 ARG 210 A THR 211 n 195 THR 211 A LEU 212 n 196 LEU 212 A PHE 213 n 197 PHE 213 A ASP 214 n 198 ASP 214 A VAL 215 n 199 VAL 215 A LEU 216 n 200 LEU 216 A ASP 217 n 201 ASP 217 A ARG 218 n 202 ARG 218 A LEU 219 n 203 LEU 219 A ASP 220 n 204 ASP 220 A LYS 221 n 205 LYS 221 A ALA 222 n 206 ALA 222 A SER 223 n 207 SER 223 A MSE 224 n 208 MSE 224 A VAL 225 n 209 VAL 225 A HIS 226 n 210 HIS 226 A GLN 227 n 211 GLN 227 A ARG 228 n 212 ARG 228 A LYS 229 n 213 LYS 229 A LEU 230 n 214 LEU 230 A THR 231 n 215 THR 231 A ILE 232 n 216 ILE 232 A PRO 233 n 217 PRO 233 A PHE 234 n 218 PHE 234 A VAL 235 n 219 VAL 235 A LYS 236 n 220 LYS 236 A GLU 237 n 221 GLU 237 A MSE 238 n 222 MSE 238 A LEU 239 n 223 LEU 239 A ARG 240 n 224 ARG 240 A LEU 241 n 225 LEU 241 A n 1 0 B n 2 18 B n 3 19 B n 4 20 B n 5 21 B n 6 22 B n 7 23 B n 8 24 B n 9 25 B n 10 26 B n 11 27 B n 12 28 B n 13 29 B n 14 30 B PRO 31 n 15 PRO 31 B ALA 32 n 16 ALA 32 B ALA 33 n 17 ALA 33 B GLY 34 n 18 GLY 34 B ASN 35 n 19 ASN 35 B ASP 36 n 20 ASP 36 B GLU 37 n 21 GLU 37 B LEU 38 n 22 LEU 38 B ILE 39 n 23 ILE 39 B GLY 40 n 24 GLY 40 B ALA 41 n 25 ALA 41 B LEU 42 n 26 LEU 42 B LYS 43 n 27 LYS 43 B SER 44 n 28 SER 44 B ALA 45 n 29 ALA 45 B ALA 46 n 30 ALA 46 B SER 47 n 31 SER 47 B GLY 48 n 32 GLY 48 B ASP 49 n 33 ASP 49 B GLY 50 n 34 GLY 50 B VAL 51 n 35 VAL 51 B GLN 52 n 36 GLN 52 B ALA 53 n 37 ALA 53 B ILE 54 n 38 ILE 54 B TYR 55 n 39 TYR 55 B LEU 56 n 40 LEU 56 B TRP 57 n 41 TRP 57 B GLY 58 n 42 GLY 58 B PRO 59 n 43 PRO 59 B VAL 60 n 44 VAL 60 B LYS 61 n 45 LYS 61 B SER 62 n 46 SER 62 B GLY 63 n 47 GLY 63 B ARG 64 n 48 ARG 64 B THR 65 n 49 THR 65 B HIS 66 n 50 HIS 66 B LEU 67 n 51 LEU 67 B ILE 68 n 52 ILE 68 B HIS 69 n 53 HIS 69 B ALA 70 n 54 ALA 70 B ALA 71 n 55 ALA 71 B CYS 72 n 56 CYS 72 B ALA 73 n 57 ALA 73 B ARG 74 n 58 ARG 74 B ALA 75 n 59 ALA 75 B ASN 76 n 60 ASN 76 B GLU 77 n 61 GLU 77 B LEU 78 n 62 LEU 78 B GLU 79 n 63 GLU 79 B ARG 80 n 64 ARG 80 B ARG 81 n 65 ARG 81 B SER 82 n 66 SER 82 B PHE 83 n 67 PHE 83 B TYR 84 n 68 TYR 84 B ILE 85 n 69 ILE 85 B PRO 86 n 70 PRO 86 B LEU 87 n 71 LEU 87 B GLY 88 n 72 GLY 88 B ILE 89 n 73 ILE 89 B HIS 90 n 74 HIS 90 B ALA 91 n 75 ALA 91 B SER 92 n 76 SER 92 B ILE 93 n 77 ILE 93 B SER 94 n 78 SER 94 B THR 95 n 79 THR 95 B ALA 96 n 80 ALA 96 B LEU 97 n 81 LEU 97 B LEU 98 n 82 LEU 98 B GLU 99 n 83 GLU 99 B GLY 100 n 84 GLY 100 B LEU 101 n 85 LEU 101 B GLU 102 n 86 GLU 102 B GLN 103 n 87 GLN 103 B PHE 104 n 88 PHE 104 B ASP 105 n 89 ASP 105 B LEU 106 n 90 LEU 106 B ILE 107 n 91 ILE 107 B CYS 108 n 92 CYS 108 B ILE 109 n 93 ILE 109 B ASP 110 n 94 ASP 110 B ASP 111 n 95 ASP 111 B VAL 112 n 96 VAL 112 B ASP 113 n 97 ASP 113 B ALA 114 n 98 ALA 114 B VAL 115 n 99 VAL 115 B ALA 116 n 100 ALA 116 B GLY 117 n 101 GLY 117 B HIS 118 n 102 HIS 118 B PRO 119 n 103 PRO 119 B LEU 120 n 104 LEU 120 B TRP 121 n 105 TRP 121 B GLU 122 n 106 GLU 122 B GLU 123 n 107 GLU 123 B ALA 124 n 108 ALA 124 B ILE 125 n 109 ILE 125 B PHE 126 n 110 PHE 126 B ASP 127 n 111 ASP 127 B LEU 128 n 112 LEU 128 B TYR 129 n 113 TYR 129 B ASN 130 n 114 ASN 130 B ARG 131 n 115 ARG 131 B VAL 132 n 116 VAL 132 B ALA 133 n 117 ALA 133 B GLU 134 n 118 GLU 134 B GLN 135 n 119 GLN 135 B LYS 136 n 120 LYS 136 B ARG 137 n 121 ARG 137 B GLY 138 n 122 GLY 138 B SER 139 n 123 SER 139 B LEU 140 n 124 LEU 140 B ILE 141 n 125 ILE 141 B VAL 142 n 126 VAL 142 B SER 143 n 127 SER 143 B ALA 144 n 128 ALA 144 B SER 145 n 129 SER 145 B ALA 146 n 130 ALA 146 B SER 147 n 131 SER 147 B PRO 148 n 132 PRO 148 B MSE 149 n 133 MSE 149 B GLU 150 n 134 GLU 150 B ALA 151 n 135 ALA 151 B GLY 152 n 136 GLY 152 B PHE 153 n 137 PHE 153 B VAL 154 n 138 VAL 154 B LEU 155 n 139 LEU 155 B PRO 156 n 140 PRO 156 B ASP 157 n 141 ASP 157 B LEU 158 n 142 LEU 158 B VAL 159 n 143 VAL 159 B SER 160 n 144 SER 160 B ARG 161 n 145 ARG 161 B MSE 162 n 146 MSE 162 B HIS 163 n 147 HIS 163 B TRP 164 n 148 TRP 164 B GLY 165 n 149 GLY 165 B LEU 166 n 150 LEU 166 B THR 167 n 151 THR 167 B TYR 168 n 152 TYR 168 B GLN 169 n 153 GLN 169 B LEU 170 n 154 LEU 170 B GLN 171 n 155 GLN 171 B PRO 172 n 156 PRO 172 B MSE 173 n 157 MSE 173 B MSE 174 n 158 MSE 174 B ASP 175 n 159 ASP 175 B ASP 176 n 160 ASP 176 B GLU 177 n 161 GLU 177 B LYS 178 n 162 LYS 178 B LEU 179 n 163 LEU 179 B ALA 180 n 164 ALA 180 B ALA 181 n 165 ALA 181 B LEU 182 n 166 LEU 182 B GLN 183 n 167 GLN 183 B ARG 184 n 168 ARG 184 B ARG 185 n 169 ARG 185 B ALA 186 n 170 ALA 186 B ALA 187 n 171 ALA 187 B MSE 188 n 172 MSE 188 B ARG 189 n 173 ARG 189 B GLY 190 n 174 GLY 190 B LEU 191 n 175 LEU 191 B GLN 192 n 176 GLN 192 B LEU 193 n 177 LEU 193 B PRO 194 n 178 PRO 194 B GLU 195 n 179 GLU 195 B ASP 196 n 180 ASP 196 B VAL 197 n 181 VAL 197 B GLY 198 n 182 GLY 198 B ARG 199 n 183 ARG 199 B PHE 200 n 184 PHE 200 B LEU 201 n 185 LEU 201 B LEU 202 n 186 LEU 202 B ASN 203 n 187 ASN 203 B ARG 204 n 188 ARG 204 B MSE 205 n 189 MSE 205 B ALA 206 n 190 ALA 206 B ARG 207 n 191 ARG 207 B ASP 208 n 192 ASP 208 B LEU 209 n 193 LEU 209 B ARG 210 n 194 ARG 210 B THR 211 n 195 THR 211 B LEU 212 n 196 LEU 212 B PHE 213 n 197 PHE 213 B ASP 214 n 198 ASP 214 B VAL 215 n 199 VAL 215 B LEU 216 n 200 LEU 216 B ASP 217 n 201 ASP 217 B ARG 218 n 202 ARG 218 B LEU 219 n 203 LEU 219 B ASP 220 n 204 ASP 220 B LYS 221 n 205 LYS 221 B ALA 222 n 206 ALA 222 B SER 223 n 207 SER 223 B MSE 224 n 208 MSE 224 B VAL 225 n 209 VAL 225 B HIS 226 n 210 HIS 226 B GLN 227 n 211 GLN 227 B ARG 228 n 212 ARG 228 B LYS 229 n 213 LYS 229 B LEU 230 n 214 LEU 230 B THR 231 n 215 THR 231 B ILE 232 n 216 ILE 232 B PRO 233 n 217 PRO 233 B PHE 234 n 218 PHE 234 B VAL 235 n 219 VAL 235 B LYS 236 n 220 LYS 236 B GLU 237 n 221 GLU 237 B MSE 238 n 222 MSE 238 B LEU 239 n 223 LEU 239 B ARG 240 n 224 ARG 240 B LEU 241 n 225 LEU 241 B -0.1030 0.0296 0.0472 -0.0095 0.0889 0.0233 1.5144 1.5546 -1.2483 -0.8519 -0.0810 1.5361 0.1964 -0.6946 -0.0002 2.0440 -0.0410 0.5256 2.0654 -0.4757 2.4473 refined 40.3695 11.9674 117.9710 X-RAY DIFFRACTION 4.9755 -2.4450 -0.7820 6.7755 -0.6714 5.9025 0.1335 -0.5295 0.4594 0.6432 -0.0440 -0.0292 -0.4127 0.0451 0.0000 1.1118 0.0469 -0.0920 1.2424 -0.1298 1.2356 refined 60.5264 10.6813 116.9135 X-RAY DIFFRACTION -0.0270 0.0921 0.0773 -0.1401 -0.0090 0.0139 -0.2857 0.0089 -1.1875 0.2794 1.6830 0.6906 1.0831 -2.5249 0.0000 1.6533 0.1643 -0.2828 2.3319 0.2733 1.7208 refined 39.8913 3.2278 120.2593 X-RAY DIFFRACTION 2.7534 -1.9910 -0.7890 4.7506 0.9134 4.4168 0.3077 -0.5373 -0.5023 0.4879 0.0453 -0.1312 0.2491 0.0864 -0.0000 1.4733 0.0352 0.1231 1.3581 0.2221 1.4010 refined 23.4539 0.2123 107.6912 X-RAY DIFFRACTION 0.1295 0.1149 -0.0697 0.0079 -0.0785 0.1402 -0.1811 -1.0869 0.4450 -0.1228 -0.0698 -2.0228 -0.7776 0.2292 -0.0001 1.7112 0.1255 0.0124 1.3271 0.0141 1.9525 refined 34.3426 28.9727 100.7788 X-RAY DIFFRACTION 4.2377 -0.1440 2.7663 5.0511 -0.6066 5.7466 -0.0583 -0.4185 0.4881 0.5908 0.1286 0.3744 -0.4097 -0.3926 0.0000 1.1468 0.1063 0.0739 1.0291 -0.0101 1.2708 refined 18.1056 21.1585 97.1512 X-RAY DIFFRACTION 0.0487 -0.1098 0.1071 -0.0964 -0.1666 -0.0594 0.4861 1.1096 -1.3206 -1.3070 -0.4221 -0.1880 -0.1396 0.8859 0.0000 1.5727 -0.0207 -0.0809 1.3832 0.2286 1.9200 refined 39.7281 24.7419 91.0132 X-RAY DIFFRACTION 2.6085 -0.0952 1.3343 5.1331 0.1765 4.0871 0.2495 0.6502 0.3763 -0.1276 -0.1686 0.1020 -0.0760 -0.0650 -0.0000 1.1462 -0.0151 0.1009 1.3187 0.1014 1.2355 refined 57.3607 12.8738 93.1299 X-RAY DIFFRACTION A 30 A 35 X-RAY DIFFRACTION 1 chain A and resseq 30:35 A 36 A 168 X-RAY DIFFRACTION 2 chain A and resseq 36:168 A 169 A 175 X-RAY DIFFRACTION 3 chain A and resseq 169:175 A 176 A 241 X-RAY DIFFRACTION 4 chain A and resseq 176:241 B 31 B 38 X-RAY DIFFRACTION 5 chain B and resseq 31:38 B 39 B 168 X-RAY DIFFRACTION 6 chain B and resseq 39:168 B 169 B 175 X-RAY DIFFRACTION 7 chain B and resseq 169:175 B 176 B 241 X-RAY DIFFRACTION 8 chain B and resseq 176:241 author_and_software_defined_assembly PISA 2 dimeric gel filtration light scattering 3310 -96 21000 A MSE 149 SELENOMETHIONINE A MSE 133 MET A MSE 162 SELENOMETHIONINE A MSE 146 MET A MSE 173 SELENOMETHIONINE A MSE 157 MET A MSE 174 SELENOMETHIONINE A MSE 158 MET A MSE 188 SELENOMETHIONINE A MSE 172 MET A MSE 205 SELENOMETHIONINE A MSE 189 MET A MSE 224 SELENOMETHIONINE A MSE 208 MET A MSE 238 SELENOMETHIONINE A MSE 222 MET B MSE 149 SELENOMETHIONINE B MSE 133 MET B MSE 162 SELENOMETHIONINE B MSE 146 MET B MSE 173 SELENOMETHIONINE B MSE 157 MET B MSE 174 SELENOMETHIONINE B MSE 158 MET B MSE 188 SELENOMETHIONINE B MSE 172 MET B MSE 205 SELENOMETHIONINE B MSE 189 MET B MSE 224 SELENOMETHIONINE B MSE 208 MET B MSE 238 SELENOMETHIONINE B MSE 222 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 N PHE 83 A N PHE 67 A O CYS 108 A O CYS 92 A N ILE 109 A N ILE 93 A O ILE 141 A O ILE 125 A O VAL 142 A O VAL 126 A N LEU 56 A N LEU 40 A N ALA 53 A N ALA 37 A O LEU 166 A O LEU 150 B N PHE 83 B N PHE 67 B O CYS 108 B O CYS 92 B N ILE 109 B N ILE 93 B O SER 143 B O SER 127 B O VAL 142 B O VAL 126 B N LEU 56 B N LEU 40 B N TYR 55 B N TYR 39 B O TYR 168 B O TYR 152 1 A GLY 0 A GLY 1 1 Y 1 A VAL 18 A VAL 2 1 Y 1 A HIS 19 A HIS 3 1 Y 1 A LEU 20 A LEU 4 1 Y 1 A PRO 21 A PRO 5 1 Y 1 A ASP 22 A ASP 6 1 Y 1 A ASP 23 A ASP 7 1 Y 1 A GLU 24 A GLU 8 1 Y 1 A THR 25 A THR 9 1 Y 1 A PHE 26 A PHE 10 1 Y 1 A THR 27 A THR 11 1 Y 1 A SER 28 A SER 12 1 Y 1 A TYR 29 A TYR 13 1 Y 1 B GLY 0 B GLY 1 1 Y 1 B VAL 18 B VAL 2 1 Y 1 B HIS 19 B HIS 3 1 Y 1 B LEU 20 B LEU 4 1 Y 1 B PRO 21 B PRO 5 1 Y 1 B ASP 22 B ASP 6 1 Y 1 B ASP 23 B ASP 7 1 Y 1 B GLU 24 B GLU 8 1 Y 1 B THR 25 B THR 9 1 Y 1 B PHE 26 B PHE 10 1 Y 1 B THR 27 B THR 11 1 Y 1 B SER 28 B SER 12 1 Y 1 B TYR 29 B TYR 13 1 Y 1 B TYR 30 B TYR 14 1 Y 1 A LEU 87 -67.98 0.22 1 A ASP 175 -75.95 20.30 1 B ARG 204 -132.94 -39.51 1 B ARG 207 86.39 -18.75 199.910 121.4939 86.540 -29.6512 -0.0000 -0.0000 -29.6512 0.0000 -29.6512 1. 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. 2. SULFATE (SO4) MODELED ARE PRESENT IN CRYSTLLIZATION/CRYO CONDITION. 0.2532 0.2237 0.2267 3.0010 46.881 1449 14406 10.0600 99.9000 1.000 0.660 1.1700 1 1.390 SAD 27.6700 0.9000 1.1100 MLHL FLAT BULK SOLVENT MODEL 83.0410 0.3510 3.0010 46.881 0 3335 25 0 3310 0.002 3393 0.550 4591 0.035 511 0.002 593 14.668 1255 0.3840 0.3310 3.1082 142 1269 1411 10 100.0000 0.3507 0.3226 3.2325 141 1290 1431 10 100.0000 0.3532 0.2986 3.3796 146 1272 1418 10 100.0000 0.3324 0.2832 3.5576 144 1281 1425 10 100.0000 0.2739 0.2403 3.7804 141 1298 1439 10 100.0000 0.2958 0.2251 4.0719 144 1291 1435 10 100.0000 0.2141 0.2084 4.4811 145 1281 1426 10 100.0000 0.2322 0.1843 5.1283 148 1306 1454 10 100.0000 0.2160 0.2096 6.4560 144 1316 1460 10 100.0000 0.1943 0.1799 38.2906 154 1353 1507 10 100.0000 91.955 3.00 46.881 3SC3 14422 -3.000 0.143 1 10.680 99.900 0.014 3.000 3.170 1.6 16285 2175 1 99.900 0.014 3.170 3.280 2.7 8745 1163 1 100.000 0.014 3.280 3.410 3.6 9113 1211 1 100.000 0.014 3.410 3.570 4.9 9140 1222 1 100.000 0.014 3.570 3.760 7.5 9312 1239 1 100.000 0.014 3.760 3.990 9.8 8967 1199 1 100.000 0.014 3.990 4.290 13.1 8984 1200 1 99.900 0.014 4.290 4.720 16.3 9219 1230 1 100.000 0.014 4.720 5.390 18.2 9077 1218 1 100.000 0.014 5.390 6.750 17.7 9191 1246 1 100.000 0.014 6.750 27.2 9314 1324 1 99.400 model building D.C. & J.S. Richardson lab molprobity@kinemage.biochem.duke.edu http://kinemage.biochem.duke.edu/molprobity/ MolProbity package 3beta29 data extraction PDB deposit@deposit.rcsb.org June 10, 2010 C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ PDB_EXTRACT package 3.10 phasing George M. Sheldrick gsheldr@shelx.uni-ac.gwdg.de Fortran_77 http://shelx.uni-ac.gwdg.de/SHELX/ SHELX package phasing Eric de La Fortelle sharp-develop@globalphasing.com http://www.globalphasing.com/sharp/ SHARP package data scaling Wolfgang Kabsch http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html XSCALE package December 6, 2007 refinement P.D. Adams PDAdams@lbl.gov C++ http://www.phenix-online.org/ PHENIX package 1.4 data reduction XDS phasing SHELXD Crystal structure of a Putative DNA replication regulator Hda (Sama_1916) from SHEWANELLA AMAZONENSIS SB2B at 3.00 A resolution 1 N N 1 N N 2 N N 2 N N 2 N N 2 N N 2 N N ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. A ASN 35 A ASN 19 HELX_P A SER 47 A SER 31 1 1 13 A GLY 63 A GLY 47 HELX_P A LEU 78 A LEU 62 1 2 16 A GLY 88 A GLY 72 HELX_P A HIS 90 A HIS 74 5 3 3 A SER 94 A SER 78 HELX_P A LEU 98 A LEU 82 5 4 5 A GLY 100 A GLY 84 HELX_P A PHE 104 A PHE 88 5 5 5 A ASP 111 A ASP 95 HELX_P A ALA 116 A ALA 100 5 6 6 A HIS 118 A HIS 102 HELX_P A GLU 134 A GLU 118 1 7 17 A LEU 155 A LEU 139 HELX_P A TRP 164 A TRP 148 1 8 10 A ASP 176 A ASP 160 HELX_P A ARG 189 A ARG 173 1 9 14 A PRO 194 A PRO 178 HELX_P A MSE 205 A MSE 189 1 10 12 A ASP 208 A ASP 192 HELX_P A HIS 226 A HIS 210 1 11 19 A THR 231 A THR 215 HELX_P A LEU 239 A LEU 223 1 12 9 B ASN 35 B ASN 19 HELX_P B ALA 46 B ALA 30 1 13 12 B GLY 63 B GLY 47 HELX_P B LEU 78 B LEU 62 1 14 16 B GLY 88 B GLY 72 HELX_P B HIS 90 B HIS 74 5 15 3 B SER 94 B SER 78 HELX_P B GLU 99 B GLU 83 5 16 6 B GLY 100 B GLY 84 HELX_P B PHE 104 B PHE 88 5 17 5 B ASP 111 B ASP 95 HELX_P B ALA 116 B ALA 100 5 18 6 B HIS 118 B HIS 102 HELX_P B GLN 135 B GLN 119 1 19 18 B LEU 155 B LEU 139 HELX_P B TRP 164 B TRP 148 1 20 10 B MSE 174 B MSE 158 HELX_P B ARG 189 B ARG 173 1 21 16 B PRO 194 B PRO 178 HELX_P B ASN 203 B ASN 187 1 22 10 B ASP 208 B ASP 192 HELX_P B GLN 227 B GLN 211 1 23 20 B THR 231 B THR 215 HELX_P B LEU 239 B LEU 223 1 24 9 covale 1.328 both A PRO 148 A C PRO 132 1_555 A MSE 149 A N MSE 133 1_555 covale 1.326 both A MSE 149 A C MSE 133 1_555 A GLU 150 A N GLU 134 1_555 covale 1.328 both A ARG 161 A C ARG 145 1_555 A MSE 162 A N MSE 146 1_555 covale 1.329 both A MSE 162 A C MSE 146 1_555 A HIS 163 A N HIS 147 1_555 covale 1.326 both A PRO 172 A C PRO 156 1_555 A MSE 173 A N MSE 157 1_555 covale 1.327 both A MSE 173 A C MSE 157 1_555 A MSE 174 A N MSE 158 1_555 covale 1.329 both A MSE 174 A C MSE 158 1_555 A ASP 175 A N ASP 159 1_555 covale 1.329 both A ALA 187 A C ALA 171 1_555 A MSE 188 A N MSE 172 1_555 covale 1.328 both A MSE 188 A C MSE 172 1_555 A ARG 189 A N ARG 173 1_555 covale 1.330 both A ARG 204 A C ARG 188 1_555 A MSE 205 A N MSE 189 1_555 covale 1.329 both A MSE 205 A C MSE 189 1_555 A ALA 206 A N ALA 190 1_555 covale 1.328 both A SER 223 A C SER 207 1_555 A MSE 224 A N MSE 208 1_555 covale 1.328 both A MSE 224 A C MSE 208 1_555 A VAL 225 A N VAL 209 1_555 covale 1.330 both A GLU 237 A C GLU 221 1_555 A MSE 238 A N MSE 222 1_555 covale 1.329 both A MSE 238 A C MSE 222 1_555 A LEU 239 A N LEU 223 1_555 covale 1.328 both B PRO 148 B C PRO 132 1_555 B MSE 149 B N MSE 133 1_555 covale 1.330 both B MSE 149 B C MSE 133 1_555 B GLU 150 B N GLU 134 1_555 covale 1.329 both B ARG 161 B C ARG 145 1_555 B MSE 162 B N MSE 146 1_555 covale 1.330 both B MSE 162 B C MSE 146 1_555 B HIS 163 B N HIS 147 1_555 covale 1.328 both B PRO 172 B C PRO 156 1_555 B MSE 173 B N MSE 157 1_555 covale 1.328 both B MSE 173 B C MSE 157 1_555 B MSE 174 B N MSE 158 1_555 covale 1.330 both B MSE 174 B C MSE 158 1_555 B ASP 175 B N ASP 159 1_555 covale 1.327 both B ALA 187 B C ALA 171 1_555 B MSE 188 B N MSE 172 1_555 covale 1.328 both B MSE 188 B C MSE 172 1_555 B ARG 189 B N ARG 173 1_555 covale 1.330 both B ARG 204 B C ARG 188 1_555 B MSE 205 B N MSE 189 1_555 covale 1.328 both B MSE 205 B C MSE 189 1_555 B ALA 206 B N ALA 190 1_555 covale 1.329 both B SER 223 B C SER 207 1_555 B MSE 224 B N MSE 208 1_555 covale 1.328 both B MSE 224 B C MSE 208 1_555 B VAL 225 B N VAL 209 1_555 covale 1.331 both B GLU 237 B C GLU 221 1_555 B MSE 238 B N MSE 222 1_555 covale 1.328 both B MSE 238 B C MSE 222 1_555 B LEU 239 B N LEU 223 1_555 HYDROLASE REGULATOR, DNA BINDING PROTEIN P-loop containing nucleoside triphosphate hydrolases, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-BIOLOGY, HYDROLASE, HYDROLASE REGULATOR, DNA BINDING PROTEIN B ASP 49 B ASP 33 1 B GLY 50 B GLY 34 0.92 A1S6W5_SHEAM UNP 1 18 A1S6W5 VHLPDDETFTSYYPAAGNDELIGALKSAASGDGVQAIYLWGPVKSGRTHLIHAACARANELERRSFYIPLGIHASISTAL LEGLEQFDLICIDDVDAVAGHPLWEEAIFDLYNRVAEQKRGSLIVSASASPMEAGFVLPDLVSRMHWGLTYQLQPMMDDE KLAALQRRAAMRGLQLPEDVGRFLLNRMARDLRTLFDVLDRLDKASMVHQRKLTIPFVKEMLRL 18 241 3SC3 18 241 A1S6W5 A 1 2 225 18 241 3SC3 18 241 A1S6W5 B 1 2 225 1 expression tag GLY 0 3SC3 A A1S6W5 UNP 1 2 expression tag GLY 0 3SC3 B A1S6W5 UNP 1 5 5 parallel parallel parallel parallel parallel parallel parallel parallel A SER 82 A SER 66 A PRO 86 A PRO 70 A LEU 106 A LEU 90 A ASP 110 A ASP 94 A SER 139 A SER 123 A ALA 144 A ALA 128 A ALA 53 A ALA 37 A TRP 57 A TRP 41 A LEU 166 A LEU 150 A GLN 169 A GLN 153 B SER 82 B SER 66 B PRO 86 B PRO 70 B LEU 106 B LEU 90 B ASP 110 B ASP 94 B SER 139 B SER 123 B ALA 144 B ALA 128 B ALA 53 B ALA 37 B TRP 57 B TRP 41 B TYR 168 B TYR 152 B GLN 169 B GLN 153 BINDING SITE FOR RESIDUE SO4 A 1 A SO4 1 Software 7 BINDING SITE FOR RESIDUE SO4 A 2 A SO4 2 Software 5 BINDING SITE FOR RESIDUE SO4 B 3 B SO4 3 Software 6 BINDING SITE FOR RESIDUE SO4 B 4 B SO4 4 Software 4 BINDING SITE FOR RESIDUE SO4 B 5 B SO4 5 Software 4 A PRO 59 A PRO 43 7 1_555 A VAL 60 A VAL 44 7 1_555 A LYS 61 A LYS 45 7 1_555 A SER 62 A SER 46 7 1_555 A GLY 63 A GLY 47 7 1_555 A ARG 64 A ARG 48 7 1_555 A THR 65 A THR 49 7 1_555 A SER 147 A SER 131 5 1_555 A PRO 148 A PRO 132 5 1_555 A MSE 149 A MSE 133 5 1_555 A HIS 163 A HIS 147 5 1_555 B LYS 136 B LYS 120 5 8_656 B PRO 59 B PRO 43 6 1_555 B LYS 61 B LYS 45 6 1_555 B SER 62 B SER 46 6 1_555 B GLY 63 B GLY 47 6 1_555 B ARG 64 B ARG 48 6 1_555 B THR 65 B THR 49 6 1_555 B SER 147 B SER 131 4 1_555 B PRO 148 B PRO 132 4 1_555 B MSE 149 B MSE 133 4 1_555 B HIS 163 B HIS 147 4 1_555 B HIS 90 B HIS 74 4 1_555 B ALA 91 B ALA 75 4 1_555 B HIS 118 B HIS 102 4 1_555 B TRP 121 B TRP 105 4 1_555 197 I 2 3