data_19400 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; The structure of the Box CD enzyme reveals regulation of rRNA methylation ; _BMRB_accession_number 19400 _BMRB_flat_file_name bmr19400.str _Entry_type original _Submission_date 2013-07-31 _Accession_date 2013-07-31 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Lapinaite Audrone . . 2 Simon B. . . 3 Skjaerven L. . . 4 Rakwalska-bange M. . . 5 Gabel F. . . 6 Carlomagno T. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 80 "13C chemical shifts" 79 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-10-29 update BMRB 'update entry citation' 2013-10-08 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'The structure of the box C/D enzyme reveals regulation of RNA methylation.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 24121435 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Lapinaite Audrone . . 2 Simon Bernd . . 3 Skjaerven Lars . . 4 Rakwalska-Bange Magdalena . . 5 Gabel Frank . . 6 Carlomagno Teresa . . stop_ _Journal_abbreviation Nature _Journal_name_full Nature _Journal_volume 502 _Journal_issue 7472 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 519 _Page_last 523 _Year 2013 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'The structure of the Box CD enzyme reveals regulation of rRNA methylation' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'SSR26, 1' $SSR26 'SSR26, 2' $SSR26 'NOP5/NOP56 RELATED PROTEIN, 1' $NOP5-NOP56_RELATED_PROTEIN '50S RIBOSOMAL PROTEIN L7AE, 1' $50S_RIBOSOMAL_PROTEIN_L7AE 'FIBRILLARIN-LIKE RRNA/TRNA 2'-O-METHYLTRANSFERASE, 1' $FIBRILLARIN-LIKE_RRNA-TRNA_2'-O-METHYLTRANSFERASE 'NOP5/NOP56 RELATED PROTEIN, 2' $NOP5-NOP56_RELATED_PROTEIN '50S RIBOSOMAL PROTEIN L7AE, 2' $50S_RIBOSOMAL_PROTEIN_L7AE 'FIBRILLARIN-LIKE RRNA/TRNA 2'-O-METHYLTRANSFERASE, 2' $FIBRILLARIN-LIKE_RRNA-TRNA_2'-O-METHYLTRANSFERASE 'NOP5/NOP56 RELATED PROTEIN, 3' $NOP5-NOP56_RELATED_PROTEIN '50S RIBOSOMAL PROTEIN L7AE, 3' $50S_RIBOSOMAL_PROTEIN_L7AE 'FIBRILLARIN-LIKE RRNA/TRNA 2'-O-METHYLTRANSFERASE, 3' $FIBRILLARIN-LIKE_RRNA-TRNA_2'-O-METHYLTRANSFERASE 'NOP5/NOP56 RELATED PROTEIN, 4' $NOP5-NOP56_RELATED_PROTEIN '50S RIBOSOMAL PROTEIN L7AE, 4' $50S_RIBOSOMAL_PROTEIN_L7AE 'FIBRILLARIN-LIKE RRNA/TRNA 2'-O-METHYLTRANSFERASE, 4' $FIBRILLARIN-LIKE_RRNA-TRNA_2'-O-METHYLTRANSFERASE '5'-R(*UP*CP*GP*CP*CP*CP*AP*UP*CP*AP*CP)-3', 1' $5'-R(*UP*CP*GP*CP*CP*CP*AP*UP*CP*AP*CP)-3' '5'-R(*UP*CP*GP*CP*CP*CP*AP*UP*CP*AP*CP)-3', 2' $5'-R(*UP*CP*GP*CP*CP*CP*AP*UP*CP*AP*CP)-3' '5'-R(*UP*CP*GP*CP*CP*CP*AP*UP*CP*AP*CP)-3', 3' $5'-R(*UP*CP*GP*CP*CP*CP*AP*UP*CP*AP*CP)-3' '5'-R(*UP*CP*GP*CP*CP*CP*AP*UP*CP*AP*CP)-3', 4' $5'-R(*UP*CP*GP*CP*CP*CP*AP*UP*CP*AP*CP)-3' stop_ _System_molecular_weight 385350.03588 _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state 'all free' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_SSR26 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common SSR26 _Molecular_mass 23589.23362 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 72 _Mol_residue_sequence ; GCGAGCAAUGAUGAGUGAUG GGCGAACUGAGCUCGAAAGA GCAAUGAUGAGUGAUGGGCG AACUGAGCUCGC ; loop_ _Residue_seq_code _Residue_label 1 G 2 C 3 G 4 A 5 G 6 C 7 A 8 A 9 U 10 G 11 A 12 U 13 G 14 A 15 G 16 U 17 G 18 A 19 U 20 G 21 G 22 G 23 C 24 G 25 A 26 A 27 C 28 U 29 G 30 A 31 G 32 C 33 U 34 C 35 G 36 A 37 A 38 A 39 G 40 A 41 G 42 C 43 A 44 A 45 U 46 G 47 A 48 U 49 G 50 A 51 G 52 U 53 G 54 A 55 U 56 G 57 G 58 G 59 C 60 G 61 A 62 A 63 C 64 U 65 G 66 A 67 G 68 C 69 U 70 C 71 G 72 C stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value PDB 4BY9 4BY9 . . . . . stop_ save_ save_NOP5-NOP56_RELATED_PROTEIN _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common NOP5-NOP56_RELATED_PROTEIN _Molecular_mass 42138.6332 _Mol_thiol_state 'all free' _Details . _Residue_count 366 _Mol_residue_sequence ; FISENVRGIYAFDENGNLIE KRYFTDKPEKVLDQLLKGEI TKDLEELLNSLKEKGYDEFV FEHPCLSRRAKELGFSATTE FPNIAGERLRSNPCEFLGEN WFEEYYKVGVALTRMRIQEQ SGARDKMVIQAIEALDDVDK VINLLVARLREWYSLHFPEL DELLPKHPQYVAFVKTVGHR DNINEEVLRCLGLSECKIKK ILEAKEKTMGAWMDQTDIEV VRQLAEEIDRLYQLRKKLED YIDRAMCDVAPNLKALVGAK LAARLISLAGGLRELAMMPS STIQVLGAEKALFRHLRTGA KPPKHGVIYQYPAINRSPWW QRGKIARALAGKLAIAARVD YFCGEYIAEELKKELEARIR EIKEKY ; loop_ _Residue_seq_code _Residue_label 1 PHE 2 ILE 3 SER 4 GLU 5 ASN 6 VAL 7 ARG 8 GLY 9 ILE 10 TYR 11 ALA 12 PHE 13 ASP 14 GLU 15 ASN 16 GLY 17 ASN 18 LEU 19 ILE 20 GLU 21 LYS 22 ARG 23 TYR 24 PHE 25 THR 26 ASP 27 LYS 28 PRO 29 GLU 30 LYS 31 VAL 32 LEU 33 ASP 34 GLN 35 LEU 36 LEU 37 LYS 38 GLY 39 GLU 40 ILE 41 THR 42 LYS 43 ASP 44 LEU 45 GLU 46 GLU 47 LEU 48 LEU 49 ASN 50 SER 51 LEU 52 LYS 53 GLU 54 LYS 55 GLY 56 TYR 57 ASP 58 GLU 59 PHE 60 VAL 61 PHE 62 GLU 63 HIS 64 PRO 65 CYS 66 LEU 67 SER 68 ARG 69 ARG 70 ALA 71 LYS 72 GLU 73 LEU 74 GLY 75 PHE 76 SER 77 ALA 78 THR 79 THR 80 GLU 81 PHE 82 PRO 83 ASN 84 ILE 85 ALA 86 GLY 87 GLU 88 ARG 89 LEU 90 ARG 91 SER 92 ASN 93 PRO 94 CYS 95 GLU 96 PHE 97 LEU 98 GLY 99 GLU 100 ASN 101 TRP 102 PHE 103 GLU 104 GLU 105 TYR 106 TYR 107 LYS 108 VAL 109 GLY 110 VAL 111 ALA 112 LEU 113 THR 114 ARG 115 MET 116 ARG 117 ILE 118 GLN 119 GLU 120 GLN 121 SER 122 GLY 123 ALA 124 ARG 125 ASP 126 LYS 127 MET 128 VAL 129 ILE 130 GLN 131 ALA 132 ILE 133 GLU 134 ALA 135 LEU 136 ASP 137 ASP 138 VAL 139 ASP 140 LYS 141 VAL 142 ILE 143 ASN 144 LEU 145 LEU 146 VAL 147 ALA 148 ARG 149 LEU 150 ARG 151 GLU 152 TRP 153 TYR 154 SER 155 LEU 156 HIS 157 PHE 158 PRO 159 GLU 160 LEU 161 ASP 162 GLU 163 LEU 164 LEU 165 PRO 166 LYS 167 HIS 168 PRO 169 GLN 170 TYR 171 VAL 172 ALA 173 PHE 174 VAL 175 LYS 176 THR 177 VAL 178 GLY 179 HIS 180 ARG 181 ASP 182 ASN 183 ILE 184 ASN 185 GLU 186 GLU 187 VAL 188 LEU 189 ARG 190 CYS 191 LEU 192 GLY 193 LEU 194 SER 195 GLU 196 CYS 197 LYS 198 ILE 199 LYS 200 LYS 201 ILE 202 LEU 203 GLU 204 ALA 205 LYS 206 GLU 207 LYS 208 THR 209 MET 210 GLY 211 ALA 212 TRP 213 MET 214 ASP 215 GLN 216 THR 217 ASP 218 ILE 219 GLU 220 VAL 221 VAL 222 ARG 223 GLN 224 LEU 225 ALA 226 GLU 227 GLU 228 ILE 229 ASP 230 ARG 231 LEU 232 TYR 233 GLN 234 LEU 235 ARG 236 LYS 237 LYS 238 LEU 239 GLU 240 ASP 241 TYR 242 ILE 243 ASP 244 ARG 245 ALA 246 MET 247 CYS 248 ASP 249 VAL 250 ALA 251 PRO 252 ASN 253 LEU 254 LYS 255 ALA 256 LEU 257 VAL 258 GLY 259 ALA 260 LYS 261 LEU 262 ALA 263 ALA 264 ARG 265 LEU 266 ILE 267 SER 268 LEU 269 ALA 270 GLY 271 GLY 272 LEU 273 ARG 274 GLU 275 LEU 276 ALA 277 MET 278 MET 279 PRO 280 SER 281 SER 282 THR 283 ILE 284 GLN 285 VAL 286 LEU 287 GLY 288 ALA 289 GLU 290 LYS 291 ALA 292 LEU 293 PHE 294 ARG 295 HIS 296 LEU 297 ARG 298 THR 299 GLY 300 ALA 301 LYS 302 PRO 303 PRO 304 LYS 305 HIS 306 GLY 307 VAL 308 ILE 309 TYR 310 GLN 311 TYR 312 PRO 313 ALA 314 ILE 315 ASN 316 ARG 317 SER 318 PRO 319 TRP 320 TRP 321 GLN 322 ARG 323 GLY 324 LYS 325 ILE 326 ALA 327 ARG 328 ALA 329 LEU 330 ALA 331 GLY 332 LYS 333 LEU 334 ALA 335 ILE 336 ALA 337 ALA 338 ARG 339 VAL 340 ASP 341 TYR 342 PHE 343 CYS 344 GLY 345 GLU 346 TYR 347 ILE 348 ALA 349 GLU 350 GLU 351 LEU 352 LYS 353 LYS 354 GLU 355 LEU 356 GLU 357 ALA 358 ARG 359 ILE 360 ARG 361 GLU 362 ILE 363 LYS 364 GLU 365 LYS 366 TYR stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-11-04 loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value PDB 2NNW "Alternative Conformations Of Nop56/58-fibrillarin Complex And Implication For Induced-fit Assenly Of Box C/d Rnps" 99.18 376 98.35 98.35 0.00e+00 PDB 3NMU "Crystal Structure Of Substrate-Bound Halfmer Box CD RNP" 100.00 379 98.36 98.36 0.00e+00 PDB 3NVI "Structure Of N-terminal Truncated Nop56/58 Bound With L7ae And Box C/d Rna" 100.00 379 98.36 98.36 0.00e+00 PDB 3NVK "Structural Basis For Substrate Placement By An Archaeal Box CD Ribonucleoprotein Particle" 98.36 376 98.33 98.33 0.00e+00 PDB 4BY9 "The Structure Of The Box Cd Enzyme Reveals Regulation Of Rrna Methylation" 99.73 366 98.36 98.36 0.00e+00 GB AAL80184 "NOP5/NOP56 related protein [Pyrococcus furiosus DSM 3638]" 100.00 402 98.36 98.36 0.00e+00 GB AFN04514 "C/D box methylation guide ribonucleoprotein complex aNOP56 subunit [Pyrococcus furiosus COM1]" 100.00 402 98.36 98.36 0.00e+00 REF WP_011011172 "hypothetical protein [Pyrococcus furiosus]" 100.00 402 98.36 98.36 0.00e+00 stop_ save_ save_50S_RIBOSOMAL_PROTEIN_L7AE _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 50S_RIBOSOMAL_PROTEIN_L7AE _Molecular_mass 13175.4847 _Mol_thiol_state 'all free' _Details . _Residue_count 121 _Mol_residue_sequence ; KPSYVKFEVPKCLAEKALQA VEIARDTGKIRKGTNETTKA VERGCAKLVIIAEDVDPEEI VAHLPPLCEECEIPYIYVPC KKELGAAACIEVAAASVAII EPGKARDLVEEIAMKVKELM K ; loop_ _Residue_seq_code _Residue_label 1 LYS 2 PRO 3 SER 4 TYR 5 VAL 6 LYS 7 PHE 8 GLU 9 VAL 10 PRO 11 LYS 12 CYS 13 LEU 14 ALA 15 GLU 16 LYS 17 ALA 18 LEU 19 GLN 20 ALA 21 VAL 22 GLU 23 ILE 24 ALA 25 ARG 26 ASP 27 THR 28 GLY 29 LYS 30 ILE 31 ARG 32 LYS 33 GLY 34 THR 35 ASN 36 GLU 37 THR 38 THR 39 LYS 40 ALA 41 VAL 42 GLU 43 ARG 44 GLY 45 CYS 46 ALA 47 LYS 48 LEU 49 VAL 50 ILE 51 ILE 52 ALA 53 GLU 54 ASP 55 VAL 56 ASP 57 PRO 58 GLU 59 GLU 60 ILE 61 VAL 62 ALA 63 HIS 64 LEU 65 PRO 66 PRO 67 LEU 68 CYS 69 GLU 70 GLU 71 CYS 72 GLU 73 ILE 74 PRO 75 TYR 76 ILE 77 TYR 78 VAL 79 PRO 80 CYS 81 LYS 82 LYS 83 GLU 84 LEU 85 GLY 86 ALA 87 ALA 88 ALA 89 CYS 90 ILE 91 GLU 92 VAL 93 ALA 94 ALA 95 ALA 96 SER 97 VAL 98 ALA 99 ILE 100 ILE 101 GLU 102 PRO 103 GLY 104 LYS 105 ALA 106 ARG 107 ASP 108 LEU 109 VAL 110 GLU 111 GLU 112 ILE 113 ALA 114 MET 115 LYS 116 VAL 117 LYS 118 GLU 119 LEU 120 MET 121 LYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value UNP RL7A_PYRFU Q8U160 . . . . . stop_ save_ save_FIBRILLARIN-LIKE_RRNA-TRNA_2'-O-METHYLTRANSFERASE _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common FIBRILLARIN-LIKE_RRNA-TRNA_2'-O-METHYLTRANSFERASE _Molecular_mass 25762.6891 _Mol_thiol_state 'not present' _Details . _Residue_count 227 _Mol_residue_sequence ; MVEVKKHKFPGVYVVIDDDG SEKIATKNLVPGQRVYGERV IKWEGEEYRIWNPHRSKLGA AIVNGLKNFPIKPGKSVLYL GIASGTTASHVSDIVGWEGK IYGIEFSPRVLRELVPIVEE RRNIIPILGDATKPEEYRAL VTKVDVIFEDVAQPTQAKIL IDNAKAYLKRGGYGMIAVKS RSIDVTKEPEQVFKEVEREL SEYFEVIERLNLEPYEKDHA LFVVRKP ; loop_ _Residue_seq_code _Residue_label 1 MET 2 VAL 3 GLU 4 VAL 5 LYS 6 LYS 7 HIS 8 LYS 9 PHE 10 PRO 11 GLY 12 VAL 13 TYR 14 VAL 15 VAL 16 ILE 17 ASP 18 ASP 19 ASP 20 GLY 21 SER 22 GLU 23 LYS 24 ILE 25 ALA 26 THR 27 LYS 28 ASN 29 LEU 30 VAL 31 PRO 32 GLY 33 GLN 34 ARG 35 VAL 36 TYR 37 GLY 38 GLU 39 ARG 40 VAL 41 ILE 42 LYS 43 TRP 44 GLU 45 GLY 46 GLU 47 GLU 48 TYR 49 ARG 50 ILE 51 TRP 52 ASN 53 PRO 54 HIS 55 ARG 56 SER 57 LYS 58 LEU 59 GLY 60 ALA 61 ALA 62 ILE 63 VAL 64 ASN 65 GLY 66 LEU 67 LYS 68 ASN 69 PHE 70 PRO 71 ILE 72 LYS 73 PRO 74 GLY 75 LYS 76 SER 77 VAL 78 LEU 79 TYR 80 LEU 81 GLY 82 ILE 83 ALA 84 SER 85 GLY 86 THR 87 THR 88 ALA 89 SER 90 HIS 91 VAL 92 SER 93 ASP 94 ILE 95 VAL 96 GLY 97 TRP 98 GLU 99 GLY 100 LYS 101 ILE 102 TYR 103 GLY 104 ILE 105 GLU 106 PHE 107 SER 108 PRO 109 ARG 110 VAL 111 LEU 112 ARG 113 GLU 114 LEU 115 VAL 116 PRO 117 ILE 118 VAL 119 GLU 120 GLU 121 ARG 122 ARG 123 ASN 124 ILE 125 ILE 126 PRO 127 ILE 128 LEU 129 GLY 130 ASP 131 ALA 132 THR 133 LYS 134 PRO 135 GLU 136 GLU 137 TYR 138 ARG 139 ALA 140 LEU 141 VAL 142 THR 143 LYS 144 VAL 145 ASP 146 VAL 147 ILE 148 PHE 149 GLU 150 ASP 151 VAL 152 ALA 153 GLN 154 PRO 155 THR 156 GLN 157 ALA 158 LYS 159 ILE 160 LEU 161 ILE 162 ASP 163 ASN 164 ALA 165 LYS 166 ALA 167 TYR 168 LEU 169 LYS 170 ARG 171 GLY 172 GLY 173 TYR 174 GLY 175 MET 176 ILE 177 ALA 178 VAL 179 LYS 180 SER 181 ARG 182 SER 183 ILE 184 ASP 185 VAL 186 THR 187 LYS 188 GLU 189 PRO 190 GLU 191 GLN 192 VAL 193 PHE 194 LYS 195 GLU 196 VAL 197 GLU 198 ARG 199 GLU 200 LEU 201 SER 202 GLU 203 TYR 204 PHE 205 GLU 206 VAL 207 ILE 208 GLU 209 ARG 210 LEU 211 ASN 212 LEU 213 GLU 214 PRO 215 TYR 216 GLU 217 LYS 218 ASP 219 HIS 220 ALA 221 LEU 222 PHE 223 VAL 224 VAL 225 ARG 226 LYS 227 PRO stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-11-04 loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value PDB 1PRY "Structure Determination Of Fibrillarin Homologue From Hyperthermophilic Archaeon Pyrococcus Furiosus (Pfu-65527)" 100.00 227 99.56 99.56 2.48e-158 PDB 2NNW "Alternative Conformations Of Nop56/58-fibrillarin Complex And Implication For Induced-fit Assenly Of Box C/d Rnps" 100.00 234 100.00 100.00 1.04e-159 PDB 3NMU "Crystal Structure Of Substrate-Bound Halfmer Box CD RNP" 100.00 234 100.00 100.00 1.04e-159 PDB 3NVK "Structural Basis For Substrate Placement By An Archaeal Box CD Ribonucleoprotein Particle" 100.00 234 100.00 100.00 1.04e-159 PDB 3NVM "Structural Basis For Substrate Placement By An Archaeal Box CD Ribonucleoprotein Particle" 100.00 234 100.00 100.00 1.04e-159 PDB 4BY9 "The Structure Of The Box Cd Enzyme Reveals Regulation Of Rrna Methylation" 100.00 227 100.00 100.00 2.07e-159 GB AAL80183 "fibrillarin-like pre-rRNA processing protein [Pyrococcus furiosus DSM 3638]" 100.00 227 100.00 100.00 2.07e-159 GB AFN04515 "fibrillarin [Pyrococcus furiosus COM1]" 100.00 227 100.00 100.00 2.07e-159 REF WP_011011171 "fibrillarin-like rRNA methylase [Pyrococcus furiosus]" 100.00 227 100.00 100.00 2.07e-159 SP Q8U4M2 "RecName: Full=Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase" 100.00 227 100.00 100.00 2.07e-159 stop_ save_ save_5'-R(*UP*CP*GP*CP*CP*CP*AP*UP*CP*AP*CP)-3' _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common 5'-R(*UP*CP*GP*CP*CP*CP*AP*UP*CP*AP*CP)-3' _Molecular_mass 3466.08516 _Mol_thiol_state 'not present' _Details . _Residue_count 11 _Mol_residue_sequence UCGCCCAUCAC loop_ _Residue_seq_code _Residue_label 1 U 2 C 3 G 4 C 5 C 6 C 7 A 8 U 9 C 10 A 11 C stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value PDB 4BY9 4BY9 . . . . . stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $5'-R(*UP*CP*GP*CP*CP*CP*AP*UP*CP*AP*CP)-3' 'Pyrococcus furiosus' 2261 Archaea . Pyrococcus furiosus $50S_RIBOSOMAL_PROTEIN_L7AE 'Pyrococcus furiosus' 2261 Archaea . Pyrococcus furiosus $FIBRILLARIN-LIKE_RRNA-TRNA_2'-O-METHYLTRANSFERASE 'Pyrococcus furiosus' 2261 Archaea . Pyrococcus furiosus $NOP5-NOP56_RELATED_PROTEIN 'Pyrococcus furiosus' 2261 Archaea . Pyrococcus furiosus $SSR26 'Pyrococcus furiosus' 2261 Archaea . Pyrococcus furiosus stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_type _Vector_name $5'-R(*UP*CP*GP*CP*CP*CP*AP*UP*CP*AP*CP)-3' 'chemical synthesis' . . . . n/a . $50S_RIBOSOMAL_PROTEIN_L7AE 'recombinant technology' 'Escherichia coli' . . 'BL21 Rosetta 2' n/a . $FIBRILLARIN-LIKE_RRNA-TRNA_2'-O-METHYLTRANSFERASE 'recombinant technology' 'Escherichia coli' . . 'BL21 DE3' n/a . $NOP5-NOP56_RELATED_PROTEIN 'recombinant technology' . . . 'BL21 DE3' n/a . $SSR26 'chemical synthesis' 'ESCHERICHIA COLI' . . . n/a . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details 0.014-0.03mmol/l loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $SSR26 . mM 0.014 0.03 'natural abundance' $NOP5-NOP56_RELATED_PROTEIN . mM 0.014 0.03 'natural abundance' $50S_RIBOSOMAL_PROTEIN_L7AE . mM 0.014 0.03 'natural abundance' $FIBRILLARIN-LIKE_RRNA-TRNA_2'-O-METHYLTRANSFERASE . mM 0.014 0.03 [U-13C] $5'-R(*UP*CP*GP*CP*CP*CP*AP*UP*CP*AP*CP)-3' . mM 0.014 0.03 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_AutoDep _Saveframe_category software _Name AutoDep _Version 4.3 loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_CNS _Saveframe_category software _Name CNS _Version 1.2 loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_NMRView _Saveframe_category software _Name NMRView _Version any loop_ _Task 'chemical shift assignment' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_Bruker_Avance-800 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _Details . save_ ############################# # NMR applied experiments # ############################# save_13C,1H-HMQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name 13C,1H-HMQC _Sample_label $sample_1 save_ save_NMR_spectrometer_expt _Saveframe_category NMR_applied_experiment _Experiment_name . _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details 'pH [6.6], temp [328], pressure [0.0], ionStrength [0.0]' loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 0.0 . mM pH 6.600 . pH pressure 1 . atm temperature 328.000 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference _Details . loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis _Indirect_shift_ratio HDO C 13 HDO ppm 4.486 internal indirect . . . 0.25144953 HDO H 1 HDO ppm 4.486 internal indirect . . . 1 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_assigned_chem_shift_list _Saveframe_category assigned_chemical_shifts _Details 'Origin nmrStar file /ebi/msd/pdb_root/Processing/prepare/4by9/ebi/full_fib_csh.str.csh' loop_ _Experiment_label 13C,1H-HMQC stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'FIBRILLARIN-LIKE RRNA/TRNA 2'-O-METHYLTRANSFERASE, 1' _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 2 2 VAL HG1 H 1.0121 0.01 2 2 2 2 VAL CG1 C 24.9135 0.09 2 3 4 4 VAL HG1 H -0.0775 0.01 2 4 4 4 VAL HG2 H -0.0287 0.01 2 5 4 4 VAL CG1 C 18.9473 0.09 2 6 4 4 VAL CG2 C 17.7473 0.09 2 7 12 12 VAL HG1 H 1.0960 0.01 2 8 12 12 VAL CG1 C 20.5670 0.09 2 9 14 14 VAL HG1 H 0.7516 0.01 2 10 14 14 VAL CG1 C 17.9234 0.09 2 11 15 15 VAL HG1 H 0.9842 0.01 2 12 15 15 VAL HG2 H 0.6838 0.01 2 13 15 15 VAL CG1 C 20.5504 0.09 2 14 15 15 VAL CG2 C 18.6719 0.09 2 15 16 16 ILE HD1 H 0.8424 0.01 1 16 16 16 ILE CD1 C 10.0074 0.09 1 17 24 24 ILE HD1 H 0.3749 0.01 1 18 24 24 ILE CD1 C 11.1343 0.09 1 19 29 29 LEU HD1 H 1.0135 0.01 2 20 29 29 LEU CD1 C 22.8605 0.09 2 21 35 35 VAL HG1 H 0.9858 0.01 2 22 35 35 VAL HG2 H 0.9409 0.01 2 23 35 35 VAL CG1 C 19.1840 0.09 2 24 35 35 VAL CG2 C 18.8917 0.09 2 25 40 40 VAL HG1 H 1.0824 0.01 2 26 40 40 VAL HG2 H 0.9873 0.01 2 27 40 40 VAL CG1 C 18.1850 0.09 2 28 40 40 VAL CG2 C 18.6989 0.09 2 29 41 41 ILE HD1 H 0.8412 0.01 1 30 41 41 ILE CD1 C 11.6505 0.09 1 31 50 50 ILE HD1 H 0.8497 0.01 1 32 50 50 ILE CD1 C 8.6317 0.09 1 33 58 58 LEU HD1 H 0.9603 0.01 2 34 58 58 LEU HD2 H 0.7867 0.01 2 35 58 58 LEU CD1 C 19.4133 0.09 2 36 58 58 LEU CD2 C 21.6870 0.09 2 37 62 62 ILE HD1 H -0.2084 0.01 1 38 62 62 ILE CD1 C 10.5396 0.09 1 39 63 63 VAL HG1 H 0.8787 0.01 2 40 63 63 VAL CG1 C 19.3991 0.09 2 41 66 66 LEU HD1 H 0.7003 0.01 2 42 66 66 LEU HD2 H 0.8283 0.01 2 43 66 66 LEU CD1 C 24.8199 0.09 2 44 66 66 LEU CD2 C 17.0984 0.09 2 45 71 71 ILE HD1 H 0.8370 0.01 1 46 71 71 ILE CD1 C 10.7681 0.09 1 47 77 77 VAL HG1 H 1.3275 0.01 2 48 77 77 VAL CG1 C 20.8033 0.09 2 49 78 78 LEU HD1 H 0.9816 0.01 2 50 78 78 LEU HD2 H 0.9691 0.01 2 51 78 78 LEU CD1 C 24.1736 0.09 2 52 78 78 LEU CD2 C 18.4947 0.09 2 53 80 80 LEU HD1 H 1.1445 0.01 2 54 80 80 LEU HD2 H 0.9491 0.01 2 55 80 80 LEU CD1 C 24.4254 0.09 2 56 80 80 LEU CD2 C 20.8183 0.09 2 57 82 82 ILE HD1 H 0.5687 0.01 1 58 82 82 ILE CD1 C 13.1383 0.09 1 59 91 91 VAL HG1 H 1.2854 0.01 2 60 91 91 VAL HG2 H 1.0214 0.01 2 61 91 91 VAL CG1 C 16.0625 0.09 2 62 91 91 VAL CG2 C 17.8583 0.09 2 63 94 94 ILE HD1 H 1.1519 0.01 1 64 94 94 ILE CD1 C 12.5332 0.09 1 65 95 95 VAL HG1 H 0.8770 0.01 2 66 95 95 VAL CG1 C 18.3516 0.09 2 67 101 101 ILE HD1 H 0.7460 0.01 1 68 101 101 ILE CD1 C 12.7293 0.09 1 69 104 104 ILE HD1 H 0.0031 0.01 1 70 104 104 ILE CD1 C 7.0681 0.09 1 71 110 110 VAL HG1 H 1.1253 0.01 2 72 110 110 VAL HG2 H 1.0527 0.01 2 73 110 110 VAL CG1 C 20.7938 0.09 2 74 110 110 VAL CG2 C 22.0140 0.09 2 75 111 111 LEU HD1 H 1.0156 0.01 2 76 111 111 LEU HD2 H 1.1175 0.01 2 77 111 111 LEU CD1 C 23.9127 0.09 2 78 111 111 LEU CD2 C 21.7416 0.09 2 79 114 114 LEU HD2 H 0.8683 0.01 2 80 114 114 LEU CD2 C 23.4029 0.09 2 81 117 117 ILE HD1 H 0.8022 0.01 1 82 117 117 ILE CD1 C 10.4338 0.09 1 83 118 118 VAL HG1 H 1.0865 0.01 2 84 118 118 VAL HG2 H 0.9734 0.01 2 85 118 118 VAL CG1 C 19.3122 0.09 2 86 118 118 VAL CG2 C 19.7028 0.09 2 87 124 124 ILE HD1 H 0.6854 0.01 1 88 124 124 ILE CD1 C 10.7741 0.09 1 89 125 125 ILE HD1 H 1.1678 0.01 1 90 125 125 ILE CD1 C 9.7635 0.09 1 91 127 127 ILE HD1 H 0.9276 0.01 1 92 127 127 ILE CD1 C 12.1916 0.09 1 93 141 141 VAL HG1 H 1.3557 0.01 2 94 141 141 VAL HG2 H 0.2628 0.01 2 95 141 141 VAL CG1 C 24.6430 0.09 2 96 141 141 VAL CG2 C 15.8012 0.09 2 97 144 144 VAL HG1 H 1.0989 0.01 2 98 144 144 VAL HG2 H 1.0960 0.01 2 99 144 144 VAL CG1 C 22.3870 0.09 2 100 144 144 VAL CG2 C 15.8337 0.09 2 101 147 147 ILE HD1 H 1.1236 0.01 1 102 147 147 ILE CD1 C 12.2104 0.09 1 103 151 151 VAL HG1 H 1.2361 0.01 2 104 151 151 VAL HG2 H 1.0413 0.01 2 105 151 151 VAL CG1 C 19.0897 0.09 2 106 151 151 VAL CG2 C 20.4482 0.09 2 107 159 159 ILE HD1 H 1.0711 0.01 1 108 159 159 ILE CD1 C 11.3168 0.09 1 109 160 160 LEU HD1 H 0.6592 0.01 2 110 160 160 LEU HD2 H 1.1150 0.01 2 111 160 160 LEU CD1 C 22.7083 0.09 2 112 161 161 ILE HD1 H -0.1502 0.01 1 113 161 161 ILE CD1 C 14.5356 0.09 1 114 168 168 LEU HD1 H 1.4226 0.01 2 115 168 168 LEU HD2 H 1.2409 0.01 2 116 168 168 LEU CD1 C 19.0879 0.09 2 117 168 168 LEU CD2 C 18.7245 0.09 2 118 176 176 ILE HD1 H 0.7455 0.01 1 119 176 176 ILE CD1 C 11.5892 0.09 1 120 178 178 VAL HG1 H 1.2782 0.01 2 121 178 178 VAL CG1 C 21.1556 0.09 2 122 183 183 ILE HD1 H 0.9013 0.01 1 123 183 183 ILE CD1 C 11.6841 0.09 1 124 185 185 VAL HG1 H 1.2214 0.01 2 125 185 185 VAL HG2 H 1.2347 0.01 2 126 185 185 VAL CG1 C 18.3102 0.09 2 127 185 185 VAL CG2 C 18.3938 0.09 2 128 192 192 VAL HG1 H 1.0389 0.01 2 129 192 192 VAL HG2 H 1.1068 0.01 2 130 192 192 VAL CG1 C 20.7293 0.09 2 131 192 192 VAL CG2 C 18.3712 0.09 2 132 196 196 VAL HG1 H 0.8548 0.01 2 133 196 196 VAL HG2 H 0.6394 0.01 2 134 196 196 VAL CG1 C 19.0985 0.09 2 135 196 196 VAL CG2 C 18.7071 0.09 2 136 200 200 LEU HD1 H 0.9084 0.01 2 137 200 200 LEU HD2 H 0.4141 0.01 2 138 200 200 LEU CD1 C 23.0388 0.09 2 139 200 200 LEU CD2 C 23.2615 0.09 2 140 206 206 VAL HG1 H 1.2003 0.01 2 141 206 206 VAL HG2 H 1.1617 0.01 2 142 206 206 VAL CG1 C 18.7204 0.09 2 143 206 206 VAL CG2 C 18.3346 0.09 2 144 207 207 ILE HD1 H 0.9981 0.01 1 145 207 207 ILE CD1 C 9.2714 0.09 1 146 210 210 LEU HD1 H 0.9208 0.01 2 147 210 210 LEU CD1 C 24.3552 0.09 2 148 212 212 LEU HD1 H 0.9294 0.01 2 149 212 212 LEU CD1 C 22.1580 0.09 2 150 221 221 LEU HD1 H 0.9457 0.01 2 151 221 221 LEU HD2 H 0.2108 0.01 2 152 221 221 LEU CD1 C 19.2793 0.09 2 153 221 221 LEU CD2 C 20.4908 0.09 2 154 223 223 VAL HG1 H -0.3274 0.01 2 155 223 223 VAL CG1 C 22.3567 0.09 2 156 224 224 VAL HG1 H 0.9947 0.01 2 157 224 224 VAL HG2 H 0.8655 0.01 2 158 224 224 VAL CG1 C 24.5455 0.09 2 159 224 224 VAL CG2 C 19.8461 0.09 2 stop_ save_