0.029207 0.000000 0.000000 0.000000 0.028493 0.000000 0.000000 0.000000 0.022801 0.00000 0.00000 0.00000 Gardberg, A.S. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 90.00 90.00 34.238 35.096 43.858 C3 H7 N O2 89.093 y ALANINE 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 D2 O 20.028 DEUTERATED WATER non-polymer Fe 3 55.845 FE (III) ION non-polymer C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE 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 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 N 1 N N N 2 S C N 3 N C N 4 N O N 5 N C N 6 N O N 7 N H N 8 N H N 9 N H N 10 N H N 11 N H N 12 N H N 13 N H N 14 N N N 15 S C N 16 N C N 17 N O N 18 N C N 19 N C N 20 N O N 21 N N N 22 N O N 23 N H N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N N N 32 S C N 33 N C N 34 N O N 35 N C N 36 N C N 37 N O N 38 N O N 39 N O N 40 N H N 41 N H N 42 N H N 43 N H N 44 N H N 45 N H N 46 N H N 47 N N N 48 R C N 49 N C N 50 N O N 51 N C N 52 N S N 53 N O N 54 N H N 55 N H N 56 N H N 57 N H N 58 N H N 59 N H N 60 N H N 61 N O N 62 N D N 63 N D N 64 N FE N 65 N N N 66 S C N 67 N C N 68 N O N 69 N C N 70 N C N 71 N C N 72 N O N 73 N O N 74 N O N 75 N H N 76 N H N 77 N H N 78 N H N 79 N H N 80 N H N 81 N H N 82 N H N 83 N H N 84 N N N 85 N C N 86 N C N 87 N O N 88 N O N 89 N H N 90 N H N 91 N H N 92 N H N 93 N H N 94 N N N 95 S C N 96 N C N 97 N O N 98 S C N 99 N C N 100 N C N 101 N C N 102 N O N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N H N 109 N H N 110 N H N 111 N H N 112 N H N 113 N H N 114 N H N 115 N H N 116 N N N 117 S C N 118 N C N 119 N O N 120 N C N 121 N C N 122 N C N 123 N C N 124 N O N 125 N H N 126 N H N 127 N H N 128 N H N 129 N H N 130 N H N 131 N H N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N H N 138 N N N 139 S C N 140 N C N 141 N O N 142 N C N 143 N C N 144 N C N 145 N C N 146 N N N 147 N O N 148 N H N 149 N H N 150 N H N 151 N H N 152 N H N 153 N H N 154 N H N 155 N H N 156 N H N 157 N H N 158 N H N 159 N H N 160 N H N 161 N H N 162 N H N 163 N N N 164 S C N 165 N C N 166 N O N 167 N C N 168 N C N 169 N S N 170 N C N 171 N O N 172 N H N 173 N H N 174 N H N 175 N H N 176 N H N 177 N H N 178 N H N 179 N H N 180 N H N 181 N H N 182 N H N 183 N N N 184 S C N 185 N C N 186 N O N 187 N C Y 188 N C Y 189 N C Y 190 N C Y 191 N C Y 192 N C Y 193 N C N 194 N O N 195 N H N 196 N H N 197 N H N 198 N H N 199 N H N 200 N H N 201 N H N 202 N H N 203 N H N 204 N H N 205 N H N 206 N N N 207 S C N 208 N C N 209 N O N 210 N C N 211 N C N 212 N C N 213 N O N 214 N H N 215 N H N 216 N H N 217 N H N 218 N H N 219 N H N 220 N H N 221 N H N 222 N H N 223 N N N 224 S C N 225 N C N 226 N O N 227 N C N 228 N O N 229 N O N 230 N H N 231 N H N 232 N H N 233 N H N 234 N H N 235 N H N 236 N H N 237 N N N 238 S C N 239 N C N 240 N O N 241 R C N 242 N O N 243 N C N 244 N O N 245 N H N 246 N H N 247 N H N 248 N H N 249 N H N 250 N H N 251 N H N 252 N H N 253 N H N 254 N N N 255 S C N 256 N C N 257 N O N 258 N C Y 259 N C Y 260 N C Y 261 N C Y 262 N N Y 263 N C Y 264 N C Y 265 N C Y 266 N C Y 267 N C N 268 N O N 269 N H N 270 N H N 271 N H N 272 N H N 273 N H N 274 N H N 275 N H N 276 N H N 277 N H N 278 N H N 279 N H N 280 N H N 281 N N N 282 S C N 283 N C N 284 N O N 285 N C Y 286 N C Y 287 N C Y 288 N C Y 289 N C Y 290 N C Y 291 N C N 292 N O N 293 N O N 294 N H N 295 N H N 296 N H N 297 N H N 298 N H N 299 N H N 300 N H N 301 N H N 302 N H N 303 N H N 304 N H N 305 N N N 306 S C N 307 N C N 308 N O N 309 N C N 310 N C N 311 N C N 312 N O N 313 N H N 314 N H N 315 N H N 316 N H N 317 N H N 318 N H N 319 N H N 320 N H N 321 N H N 322 N H N 323 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N doub N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N doub N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N doub N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N sing N 34 N sing N 35 N doub N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N doub N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N doub N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N doub N 66 N sing N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N doub N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N doub N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N doub N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N doub N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N doub N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N sing N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N doub N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N doub N 178 N sing N 179 N sing N 180 N sing N 181 N sing Y 182 N doub Y 183 N sing Y 184 N sing N 185 N sing Y 186 N doub N 187 N sing Y 188 N doub N 189 N sing Y 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N sing N 199 N sing N 200 N doub N 201 N sing N 202 N sing N 203 N sing N 204 N sing N 205 N sing N 206 N sing N 207 N sing N 208 N sing N 209 N sing N 210 N sing N 211 N sing N 212 N sing N 213 N sing N 214 N sing N 215 N sing N 216 N sing N 217 N doub N 218 N sing N 219 N sing N 220 N sing N 221 N sing N 222 N sing N 223 N sing N 224 N sing N 225 N sing N 226 N sing N 227 N sing N 228 N sing N 229 N sing N 230 N doub N 231 N sing N 232 N sing N 233 N sing N 234 N sing N 235 N sing N 236 N sing N 237 N sing N 238 N sing N 239 N sing N 240 N sing N 241 N sing N 242 N sing N 243 N sing N 244 N sing N 245 N sing N 246 N doub N 247 N sing N 248 N sing N 249 N sing N 250 N sing Y 251 N doub Y 252 N sing Y 253 N sing N 254 N sing Y 255 N doub Y 256 N sing Y 257 N sing N 258 N sing Y 259 N sing Y 260 N doub N 261 N sing Y 262 N doub N 263 N sing Y 264 N sing N 265 N sing N 266 N sing N 267 N sing N 268 N sing N 269 N sing N 270 N sing N 271 N sing N 272 N sing N 273 N sing N 274 N doub N 275 N sing N 276 N sing N 277 N sing N 278 N sing Y 279 N doub Y 280 N sing Y 281 N sing N 282 N sing Y 283 N doub N 284 N sing Y 285 N doub N 286 N sing Y 287 N sing N 288 N sing N 289 N sing N 290 N sing N 291 N sing N 292 N sing N 293 N sing N 294 N sing N 295 N sing N 296 N sing N 297 N sing N 298 N doub N 299 N sing N 300 N sing N 301 N sing N 302 N sing N 303 N sing N 304 N sing N 305 N sing N 306 N sing N 307 N sing N 308 N sing N 309 N sing DK Acta Crystallogr.,Sect.D ABCRE6 0766 0907-4449 66 558 567 10.1107/S0907444910005494 20445231 Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallography. 2010 10.2210/pdb3kyy/pdb pdb_00003kyy 295 1 295 1 CCD 2008-03-09 MARMOSAIC 225 mm CCD IMAGE PLATE MAATEL LADI-III SINGLE WAVELENGTH x-ray 1 LAUE neutron 1 1.0 1.0 3.1 1.0 4.2 1.0 22-BM APS 1.0 SYNCHROTRON APS BEAMLINE 22-BM 3.1-4.2 NUCLEAR REACTOR 6031.728 Rubredoxin 1 man polymer 55.845 FE (III) ION 1 syn non-polymer 18.015 water 37 nat water Rd no no MAKWVCKICGYIYDEDAGDPDNGISPGTKFEELPDDWVCPICGAPKSEFEKLED MAKWVCKICGYIYDEDAGDPDNGISPGTKFEELPDDWVCPICGAPKSEFEKLED 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 Ab-initio perdeuteration sample rub, PF1282 2261 Pyrococcus furiosus 562 Escherichia coli BL21(DE3) plasmid pET24d 1 2 2.20 44.10 3.8 M sodium/potassium phosphate, hanging drop chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model pdbx_struct_conn_angle struct_conn struct_site repository Initial release Version format compliance Database references Data collection Database references Derived calculations Refinement description 1 0 2010-04-28 1 1 2011-07-13 1 2 2011-09-14 1 3 2023-09-13 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_seq_id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2009-12-07 REL REL FE FE (III) ION DOD water 1BRF PDB experimental model FE 54 2 FE FE 54 A DOD 55 3 DOD DOD 55 A DOD 56 3 DOD DOD 56 A DOD 57 3 DOD DOD 57 A DOD 58 3 DOD DOD 58 A DOD 59 3 DOD DOD 59 A DOD 60 3 DOD DOD 60 A DOD 61 3 DOD DOD 61 A DOD 62 3 DOD DOD 62 A DOD 63 3 DOD DOD 63 A DOD 64 3 DOD DOD 64 A DOD 65 3 DOD DOD 65 A DOD 66 3 DOD DOD 66 A DOD 67 3 DOD DOD 67 A DOD 68 3 DOD DOD 68 A DOD 69 3 DOD DOD 69 A DOD 70 3 DOD DOD 70 A DOD 71 3 DOD DOD 71 A DOD 72 3 DOD DOD 72 A DOD 73 3 DOD DOD 73 A DOD 74 3 DOD DOD 74 A DOD 75 3 DOD DOD 75 A DOD 76 3 DOD DOD 76 A DOD 77 3 DOD DOD 77 A DOD 78 3 DOD DOD 78 A DOD 79 3 DOD DOD 79 A DOD 80 3 DOD DOD 80 A DOD 81 3 DOD DOD 81 A DOD 82 3 DOD DOD 82 A DOD 83 3 DOD DOD 83 A DOD 84 3 DOD DOD 84 A DOD 85 3 DOD DOD 85 A DOD 86 3 DOD DOD 86 A DOD 87 3 DOD DOD 87 A DOD 88 3 DOD DOD 88 A DOD 89 3 DOD DOD 89 A DOD 90 3 DOD DOD 90 A DOD 91 3 DOD DOD 91 A MET 0 n 1 MET 0 A ALA 1 n 2 ALA 1 A LYS 2 n 3 LYS 2 A TRP 3 n 4 TRP 3 A VAL 4 n 5 VAL 4 A CYS 5 n 6 CYS 5 A LYS 6 n 7 LYS 6 A ILE 7 n 8 ILE 7 A CYS 8 n 9 CYS 8 A GLY 9 n 10 GLY 9 A TYR 10 n 11 TYR 10 A ILE 11 n 12 ILE 11 A TYR 12 n 13 TYR 12 A ASP 13 n 14 ASP 13 A GLU 14 n 15 GLU 14 A ASP 15 n 16 ASP 15 A ALA 16 n 17 ALA 16 A GLY 17 n 18 GLY 17 A ASP 18 n 19 ASP 18 A PRO 19 n 20 PRO 19 A ASP 20 n 21 ASP 20 A ASN 21 n 22 ASN 21 A GLY 22 n 23 GLY 22 A ILE 23 n 24 ILE 23 A SER 24 n 25 SER 24 A PRO 25 n 26 PRO 25 A GLY 26 n 27 GLY 26 A THR 27 n 28 THR 27 A LYS 28 n 29 LYS 28 A PHE 29 n 30 PHE 29 A GLU 30 n 31 GLU 30 A GLU 31 n 32 GLU 31 A LEU 32 n 33 LEU 32 A PRO 33 n 34 PRO 33 A ASP 34 n 35 ASP 34 A ASP 35 n 36 ASP 35 A TRP 36 n 37 TRP 36 A VAL 37 n 38 VAL 37 A CYS 38 n 39 CYS 38 A PRO 39 n 40 PRO 39 A ILE 40 n 41 ILE 40 A CYS 41 n 42 CYS 41 A GLY 42 n 43 GLY 42 A ALA 43 n 44 ALA 43 A PRO 44 n 45 PRO 44 A LYS 45 n 46 LYS 45 A SER 46 n 47 SER 46 A GLU 47 n 48 GLU 47 A PHE 48 n 49 PHE 48 A GLU 49 n 50 GLU 49 A LYS 50 n 51 LYS 50 A LEU 51 n 52 LEU 51 A GLU 52 n 53 GLU 52 A ASP 53 n 54 ASP 53 A author_and_software_defined_assembly PISA 1 monomeric A CYS 5 A SG CYS 6 1_555 A FE 54 B FE FE 1_555 A CYS 8 A SG CYS 9 1_555 112.6 A CYS 5 A SG CYS 6 1_555 A FE 54 B FE FE 1_555 A CYS 38 A SG CYS 39 1_555 111.6 A CYS 8 A SG CYS 9 1_555 A FE 54 B FE FE 1_555 A CYS 38 A SG CYS 39 1_555 103.3 A CYS 5 A SG CYS 6 1_555 A FE 54 B FE FE 1_555 A CYS 41 A SG CYS 42 1_555 104.2 A CYS 8 A SG CYS 9 1_555 A FE 54 B FE FE 1_555 A CYS 41 A SG CYS 42 1_555 113.5 A CYS 38 A SG CYS 39 1_555 A FE 54 B FE FE 1_555 A CYS 41 A SG CYS 42 1_555 111.8 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 TYR 12 A O TYR 13 A N TRP 3 A N TRP 4 A N VAL 4 A N VAL 5 A O GLU 49 A O GLU 50 1 A CE LYS 6 A CE LYS 7 1 Y 1 A NZ LYS 6 A NZ LYS 7 1 Y 1 A NZ LYS 28 A NZ LYS 29 1 Y 1 A CG ASP 53 A CG ASP 54 1 Y 1 A OD1 ASP 53 A OD1 ASP 54 1 Y 1 A OD2 ASP 53 A OD2 ASP 54 1 Y 1 A ASP 18 -154.54 66.66 16.79 0.82000 0.00000 0.00000 0.29600 0.00000 0.42500 0.156 0.145 0.145 1.10 24.51 1107 21691 5.100 98.2 0.100 1 1.350 MOLECULAR REPLACEMENT 12.770 0.90 1.11 PDB entry 1BRF ML FLAT BULK SOLVENT MODEL 40.91 0.45 -0.25000 0.00000 0.00000 0.82800 0.00000 1.53600 0.202 0.187 0.188 1.66 27.40 209 4602 4.540 69.7 2 1.090 0.90 1.11 ML FLAT BULK SOLVENT MODEL 41.30 0.60 1.10 24.51 37 452 1 0 414 0.014 856 1.426 1486 18.003 199 0.095 61 0.011 129 0.2060 0.2180 1.1500 144 2467 96.00 0.1860 0.1730 1.2110 147 2533 99.00 0.1860 0.1500 1.2870 128 2549 99.00 0.1430 0.1330 1.3860 141 2548 99.00 0.1410 0.1240 1.5250 155 2563 99.00 0.1340 0.1140 1.7460 141 2596 99.00 0.1590 0.1210 2.2000 120 2633 99.00 0.1440 0.1550 24.5140 131 2695 97.00 0.2020 0.1870 27.4060 209 4393 70.00 1.1 27.4 3KYY 21725 1 data processing Phil R. Evans pre@mrc-lmb.cam.ac.uk Fortran_77 http://www.ccp4.ac.uk/dist/html/scala.html SCALA other refinement Paul D. Adams PDAdams@lbl.gov C++ http://www.phenix-online.org/ PHENIX package data extraction PDB help@deposit.rcsb.org June 11, 2008 C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ PDB_EXTRACT package 3.005 data reduction LAUEGEN data scaling SCALA Joint Xray/neutron crystal structure determination of H-labeled perdeuterated rubredoxin at 295K 1 N N 2 N N 3 N N A ASP 18 A ASP 19 HELX_P A GLY 22 A GLY 23 5 1 5 A LYS 28 A LYS 29 HELX_P A LEU 32 A LEU 33 5 2 5 A PRO 44 A PRO 45 HELX_P A SER 46 A SER 47 5 3 3 metalc 2.298 A CYS 5 A SG CYS 6 1_555 A FE 54 B FE FE 1_555 metalc 2.272 A CYS 8 A SG CYS 9 1_555 A FE 54 B FE FE 1_555 metalc 2.308 A CYS 38 A SG CYS 39 1_555 A FE 54 B FE FE 1_555 metalc 2.263 A CYS 41 A SG CYS 42 1_555 A FE 54 B FE FE 1_555 ELECTRON TRANSPORT joint x-ray neutron refinement, Electron transport, Iron, Metal-binding, Transport RUBR_PYRFU UNP 1 1 P24297 MAKWVCKICGYIYDEDAGDPDNGISPGTKFEELPDDWVCPICGAPKSEFEKLED 1 54 3KYY 0 53 P24297 A 1 1 54 3 anti-parallel anti-parallel A ILE 11 A ILE 12 A ASP 13 A ASP 14 A LYS 2 A LYS 3 A CYS 5 A CYS 6 A PHE 48 A PHE 49 A LYS 50 A LYS 51 BINDING SITE FOR RESIDUE FE A 54 A FE 54 Software 4 A CYS 5 A CYS 6 4 1_555 A CYS 8 A CYS 9 4 1_555 A CYS 38 A CYS 39 4 1_555 A CYS 41 A CYS 42 4 1_555 19 P 21 21 21