data_5818 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; The solution structure of YbcJ from E. coli reveals a recently discovered alfaL motif involved in RNA-binding ; _BMRB_accession_number 5818 _BMRB_flat_file_name bmr5818.str _Entry_type original _Submission_date 2003-06-04 _Accession_date 2003-06-04 _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 Volpon L. . . 2 Lievre C. . . 3 Osborne M. J. . 4 Gandhi S. . . 5 Iannuzzi P. . . 6 Larocque R. . . 7 Matte A. . . 8 Cygler M. . . 9 Gehring K. . . 10 Ekiel I. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count heteronucl_NOE 1 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2003-09-12 original author . stop_ _Original_release_date 2003-09-12 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; The Solution Structure of YbcJ from Escherichia coli Reveals a Recently Discovered alphaL Motif Involved in RNA Binding ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 22721833 _PubMed_ID 12837795 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Volpon L. . . 2 Lievre C. . . 3 Osborne M. J. . 4 Gandhi S. . . 5 Iannuzzi P. . . 6 Larocque R. . . 7 Cygler M. . . 8 Gehring K. . . 9 Ekiel I. . . stop_ _Journal_abbreviation 'J. Bacteriol.' _Journal_volume 185 _Journal_issue 14 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 4204 _Page_last 4210 _Year 2003 _Details . loop_ _Keyword 'alfaL motif' 'RNA-binding protein' 'E. coli' stop_ save_ ################################## # Molecular system description # ################################## save_system_YbcJ _Saveframe_category molecular_system _Mol_system_name YbcJ _Abbreviation_common YbcJ _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label YbcJ $YbcJ stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'all free' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_YbcJ _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common YbcJ _Abbreviation_common YbcJ _Molecular_mass . _Mol_thiol_state 'all free' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 79 _Mol_residue_sequence ; GSMIHRMSNMATFSLGKHPH VELCDLLKLEGWSESGAQAK IAIAEGQVKVDGAVETRKRC KIVAGQTVSFAGHSVQVVA ; loop_ _Residue_seq_code _Residue_label 1 GLY 2 SER 3 MET 4 ILE 5 HIS 6 ARG 7 MET 8 SER 9 ASN 10 MET 11 ALA 12 THR 13 PHE 14 SER 15 LEU 16 GLY 17 LYS 18 HIS 19 PRO 20 HIS 21 VAL 22 GLU 23 LEU 24 CYS 25 ASP 26 LEU 27 LEU 28 LYS 29 LEU 30 GLU 31 GLY 32 TRP 33 SER 34 GLU 35 SER 36 GLY 37 ALA 38 GLN 39 ALA 40 LYS 41 ILE 42 ALA 43 ILE 44 ALA 45 GLU 46 GLY 47 GLN 48 VAL 49 LYS 50 VAL 51 ASP 52 GLY 53 ALA 54 VAL 55 GLU 56 THR 57 ARG 58 LYS 59 ARG 60 CYS 61 LYS 62 ILE 63 VAL 64 ALA 65 GLY 66 GLN 67 THR 68 VAL 69 SER 70 PHE 71 ALA 72 GLY 73 HIS 74 SER 75 VAL 76 GLN 77 VAL 78 VAL 79 ALA stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-01-28 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 1P9K "The Solution Structure Of Ybcj From E. Coli Reveals A Recently Discovered Alfal Motif Involved In Rna-Binding" 100.00 79 100.00 100.00 3.88e-49 DBJ BAB34013 "hypothetical protein [Escherichia coli O157:H7 str. Sakai]" 97.47 77 98.70 100.00 5.09e-47 DBJ BAE76305 "predicted RNA-binding protein [Escherichia coli str. K-12 substr. W3110]" 88.61 70 100.00 100.00 1.26e-41 DBJ BAG76077 "conserved hypothetical protein [Escherichia coli SE11]" 97.47 77 100.00 100.00 8.17e-48 DBJ BAI23895 "predicted RNA-binding protein [Escherichia coli O26:H11 str. 11368]" 88.61 70 100.00 100.00 1.26e-41 DBJ BAI29367 "predicted RNA-binding protein [Escherichia coli O103:H2 str. 12009]" 88.61 70 100.00 100.00 1.26e-41 EMBL CAP75058 "Uncharacterized protein ybcJ [Escherichia coli LF82]" 88.61 70 100.00 100.00 1.26e-41 EMBL CAQ31000 "predicted RNA-binding protein [Escherichia coli BL21(DE3)]" 88.61 70 100.00 100.00 1.26e-41 EMBL CAQ88117 "putative RNA-binding protein [Escherichia fergusonii ATCC 35469]" 88.61 70 100.00 100.00 1.26e-41 EMBL CAQ97402 "putative RNA-binding protein [Escherichia coli IAI1]" 88.61 70 100.00 100.00 1.26e-41 EMBL CAR01873 "putative RNA-binding protein [Escherichia coli S88]" 88.61 70 100.00 100.00 1.26e-41 GB AAB40281 "hypothetical 7.4kd protein [Escherichia coli]" 97.47 77 100.00 100.00 8.17e-48 GB AAC73630 "ribosome-associated protein; putative RNA-binding protein [Escherichia coli str. K-12 substr. MG1655]" 88.61 70 100.00 100.00 1.26e-41 GB AAG54885 "orf, hypothetical protein [Escherichia coli O157:H7 str. EDL933]" 97.47 77 98.70 100.00 5.09e-47 GB AAN42113 "conserved hypothetical protein [Shigella flexneri 2a str. 301]" 97.47 77 98.70 100.00 5.09e-47 GB AAN79121 "Hypothetical protein ybcJ [Escherichia coli CFT073]" 97.47 77 97.40 100.00 1.16e-46 REF NP_286277 "hypothetical protein Z0683 [Escherichia coli O157:H7 str. EDL933]" 88.61 70 100.00 100.00 1.26e-41 REF NP_308617 "hypothetical protein ECs0590 [Escherichia coli O157:H7 str. Sakai]" 88.61 70 100.00 100.00 1.26e-41 REF NP_415061 "ribosome-associated protein; putative RNA-binding protein [Escherichia coli str. K-12 substr. MG1655]" 88.61 70 100.00 100.00 1.26e-41 REF NP_706406 "hypothetical protein SF0459 [Shigella flexneri 2a str. 301]" 97.47 77 98.70 100.00 5.09e-47 REF NP_752577 "hypothetical protein c0644 [Escherichia coli CFT073]" 88.61 70 98.57 100.00 3.18e-41 SP P0AAS7 "RecName: Full=Uncharacterized protein YbcJ [Escherichia coli K-12]" 88.61 70 100.00 100.00 1.26e-41 SP P0AAS8 "RecName: Full=Uncharacterized protein YbcJ [Shigella flexneri]" 88.61 70 100.00 100.00 1.26e-41 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $YbcJ 'E. coli' 562 Eubacteria . Escherichia coli stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $YbcJ 'recombinant technology' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $YbcJ . mM 4 7 '[U-13C; U-15N]' 'phosphate buffer' 50 mM . . . NaCl 300 mM . . . DTT 15 mM . . . 'sodium azide' 1 mM . . . H2O 90 % . . . D2O 10 % . . . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $YbcJ . mM 4 7 '[U-13C; U-15N]' 'phosphate buffer' 50 mM . . . NaCl 300 mM . . . DTT 15 mM . . . 'sodium azide' 1 mM . . . 'Pf1 phage' 8 mg/mL . . . H2O 90 % . . . D2O 10 % . . . stop_ save_ ############################ # Computer software used # ############################ save_GIFA _Saveframe_category software _Name GIFA _Version 4.31 loop_ _Task processing stop_ _Details Delsuc save_ save_XWINNMR _Saveframe_category software _Name XWINNMR _Version 2.1 loop_ _Task collection stop_ _Details Bruker save_ save_XEASY _Saveframe_category software _Name XEASY _Version 1.3.13 loop_ _Task 'data analysis' stop_ _Details Bartels save_ save_TALOS _Saveframe_category software _Name TALOS _Version 2003.027.13.05 loop_ _Task refinement stop_ _Details Bax save_ save_ARIA _Saveframe_category software _Name ARIA _Version 1.1 loop_ _Task refinement stop_ _Details Nilges save_ save_CNS _Saveframe_category software _Name CNS _Version 1.1 loop_ _Task refinement stop_ _Details Brunger save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AVANCE _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label . save_ save_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label . save_ save_HNHA_3 _Saveframe_category NMR_applied_experiment _Experiment_name HNHA _Sample_label . save_ save_3D_15N-separated_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 15N-separated NOESY' _Sample_label . save_ save_IPAP-HSQ_5 _Saveframe_category NMR_applied_experiment _Experiment_name IPAP-HSQ _Sample_label . save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name HNHA _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_4 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 15N-separated NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_5 _Saveframe_category NMR_applied_experiment _Experiment_name IPAP-HSQ _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.8 . n/a temperature 313 . K 'ionic strength' 350 . mM pressure 1 . atm stop_ save_ save_heteronuclear_NOE_1 _Saveframe_category heteronuclear_NOE _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Spectrometer_frequency_1H 600 _Mol_system_component_name ? _Atom_one_atom_name . _Atom_two_atom_name . _Heteronuclear_NOE_value_type . _NOE_reference_value . _NOE_reference_description . _Text_data_format . _Text_data . loop_ _Residue_seq_code _Residue_label _Heteronuclear_NOE_value _Heteronuclear_NOE_value_error 12 THR -7.41977 1.00 13 PHE -8.24081 1.00 14 SER -10.3998 1.00 15 LEU 4.53092 1.00 16 GLY 23.8405 2.00 18 HIS 12.47 1.00 20 HIS 4.68297 1.00 21 VAL 5.86892 1.00 22 GLU 1.64208 1.00 23 LEU -8.66653 2.00 24 CYS 6.78113 1.00 25 ASP -11.6466 1.00 27 LEU 5.68642 1.00 28 LYS 1.21636 1.00 29 LEU -5.50401 1.00 30 GLU -2.88885 1.00 31 GLY 20.5868 1.00 32 TRP -11.525 1.00 38 GLN -8.51449 1.00 39 ALA 1.3988 2.00 41 ILE -7.35896 1.00 42 ALA -5.19992 2.00 43 ILE 5.41278 1.00 45 GLU -8.21041 1.00 46 GLY 8.78817 1.00 47 GLN 22.4113 2.00 48 VAL 15.6605 2.00 49 LYS -0.638585 2.00 50 VAL -7.5414 1.00 51 ASP -8.81858 1.00 53 ALA -7.11568 1.00 54 VAL -1.85495 1.00 55 GLU -4.86543 1.00 56 THR -11.7378 1.00 57 ARG 6.81151 1.00 58 LYS 2.0374 2.00 59 ARG -2.46313 1.00 61 LYS -4.4397 2.00 62 ILE -3.22334 2.00 63 VAL 0.364905 2.00 66 GLN 12.5284 1.00 67 THR -8.30163 1.00 68 VAL -4.4397 1.00 69 SER 2.46312 1.00 70 PHE 5.62565 1.00 71 ALA -3.46662 1.00 73 HIS 14.353 1.00 76 GLN -1.09472 1.00 77 VAL -7.93672 2.00 78 VAL -5.1391 1.00 79 ALA 11.008 1.00 stop_ save_