data_6107 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR structure of cross-reactive peptides from L. braziliensis ; _BMRB_accession_number 6107 _BMRB_flat_file_name bmr6107.str _Entry_type original _Submission_date 2004-02-19 _Accession_date 2004-02-19 _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 Soares M. R. . 2 Bisch P. M. . 3 'Campos de Carvalho' A. C. . 4 Valente A. P. . 5 Almeida F. C.L. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 54 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2004-04-06 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 6107 'peptide from human.' stop_ _Original_release_date 2004-04-06 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Correlation between conformation and antibody binding: NMR structure of cross-reactive peptides from T.cruzi, Human and L. braziliensis' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 14988012 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Soares M. R. . 2 Bisch P. M. . 3 'Campos de Carvalho' A. C. . 4 Valente A. P. . 5 Almeida F. C. . stop_ _Journal_abbreviation 'FEBS Lett.' _Journal_volume 560 _Journal_issue 1-3 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 134 _Page_last 140 _Year 2004 _Details . loop_ _Keyword 'Leishmania brazilienses' 'antigenic peptide' 'ribosomal p2 protein' stop_ save_ ################################## # Molecular system description # ################################## save_system_60S-ARP-P2 _Saveframe_category molecular_system _Mol_system_name '60S acidic ribosomal protein P2' _Abbreviation_common '60S acidic ribosomal protein P2' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label '60S acidic ribosomal protein P2' $60S-ARP-P2 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_60S-ARP-P2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common '60S acidic ribosomal protein P2' _Abbreviation_common '60S acidic ribosomal protein P2' _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 13 _Mol_residue_sequence EEADDDMGFGLFD loop_ _Residue_seq_code _Residue_label 1 GLU 2 GLU 3 ALA 4 ASP 5 ASP 6 ASP 7 MET 8 GLY 9 PHE 10 GLY 11 LEU 12 PHE 13 ASP stop_ _Sequence_homology_query_date 2005-11-24 _Sequence_homology_query_revised_last_date 2005-11-22 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 SWISS-PROT Q06382 'RLA3_LEIIN 60S acidic ribosomal protein P2-2' 11.71 111 100 100 6.0 SWISS-PROT Q06383 'RLA2_LEIIN 60S acidic ribosomal protein P2-1' 12.26 106 100 100 6.0 SWISS-PROT O44010 'RLA2_LEIBR 60S acidic ribosomal protein P2(Acidic ribosomal P2 beta protein) (P2B-protein)' 12.38 105 100 100 6.0 SWISS-PROT O43940 'RLA2_LEIDO 60S acidic ribosomal protein P2(Acidic ribosomal protein 1)' 12.38 105 100 100 6.0 REF XP_854050.1 'PREDICTED: similar to ribosomalprotein P1 isoform 2 [Canis familiaris]' 14.94 87 100 100 6.0 PIR B48596 "acidic ribosomal protein LiP' - Leishmaniadonovani infantum" 11.71 111 100 100 6.0 PIR A48596 'acidic ribosomal protein LiP - Leishmaniadonovani infantum' 12.26 106 100 100 6.0 GenBank AAU10518.1 'acidic ribosomal protein [Leishmaniadonovani]' 12.38 105 100 100 6.0 GenBank AAC02540.1 'acidic ribosomal P2 beta protein[Leishmania braziliensis]' 12.38 105 100 100 6.0 GenBank AAB88451.1 'acidic ribosomal protein-1; ARP-1[Leishmania donovani]' 12.38 105 100 100 6.0 EMBL CAJ06912.1 '60S acidic ribosomal protein P2,putative [Leishmania major]' 10.40 125 100 100 6.0 EMBL CAJ03348.1 '60S acidic ribosomal protein P2[Leishmania major]' 11.71 111 100 100 6.0 EMBL CAJ03347.1 '60S acidic ribosomal protein P2[Leishmania major]' 11.71 111 100 100 6.0 EMBL CAA48154.1 "acidic ribosomal protein LiP' [Leishmaniainfantum]" 11.71 111 100 100 6.0 EMBL CAJ06911.1 '60S acidic ribosomal protein P2,putative [Leishmania major]' 12.26 106 100 100 6.0 PDB 1S4H 'A Chain A, Nmr Structure Of Cross-ReactivePeptides From L. Braziliensis' 100.00 13 100 100 6.0 BMRB 6107 '60S acidic ribosomal protein P2' 100.00 13 100 100 6.0 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $60S-ARP-P2 'Leishmania braziliensis' 5660 Eukaryota . Leishmania braziliensis 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 $60S-ARP-P2 'chemical synthesis' . . . . . 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 _Isotopic_labeling $60S-ARP-P2 2 mM . 'phosphate buffer' 10 mM . H2O 90 % . D2O 10 % . stop_ save_ ############################ # Computer software used # ############################ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version 2.1 loop_ _Task processing stop_ _Details Delaglio save_ save_NMRView _Saveframe_category software _Name NMRView _Version 5.03 loop_ _Task 'data analysis' stop_ _Details 'Bruce A. Johnson' save_ save_CNS _Saveframe_category software _Name CNS _Version 1.1 loop_ _Task 'structure solution' refinement stop_ _Details Brunger save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 400 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_1 save_ save_2D_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 5.5 . n/a temperature 278 . K 'ionic strength' 10 . mM pressure 1 . atm stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _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 _Indirect_shift_ratio_citation_label _Correction_value_citation_label TSP H 1 'methyl protons' ppm 0.00 internal direct . . . 1.0 $entry_citation $entry_citation 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_chemical_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name '60S acidic ribosomal protein P2' _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 . 1 GLU H H 8.361 0.01 1 2 . 1 GLU HA H 4.053 0.01 1 3 . 1 GLU HB2 H 1.676 0.01 2 4 . 2 GLU H H 8.677 0.01 1 5 . 2 GLU HA H 4.047 0.01 1 6 . 2 GLU HB3 H 1.779 0.01 2 7 . 2 GLU HB2 H 1.655 0.01 2 8 . 2 GLU HG3 H 2.093 0.01 2 9 . 3 ALA H H 8.421 0.01 1 10 . 3 ALA HA H 3.971 0.01 1 11 . 3 ALA HB H 1.076 0.01 1 12 . 4 ASP H H 8.203 0.01 1 13 . 4 ASP HA H 4.288 0.01 1 14 . 4 ASP HB3 H 2.436 0.01 2 15 . 5 ASP H H 8.156 0.01 1 16 . 5 ASP HA H 4.288 0.01 1 17 . 5 ASP HB3 H 2.436 0.01 2 18 . 6 ASP H H 8.097 0.01 1 19 . 6 ASP HA H 4.297 0.01 1 20 . 6 ASP HB3 H 2.495 0.01 2 21 . 6 ASP HB2 H 2.445 0.01 2 22 . 7 MET H H 8.124 0.01 1 23 . 7 MET HA H 4.109 0.01 1 24 . 7 MET HB3 H 1.766 0.01 2 25 . 7 MET HB2 H 1.690 0.01 2 26 . 7 MET HG3 H 2.309 0.01 2 27 . 7 MET HG2 H 2.192 0.01 2 28 . 8 GLY H H 8.134 0.01 1 29 . 8 GLY HA3 H 3.557 0.01 2 30 . 8 GLY HA2 H 3.528 0.01 2 31 . 9 PHE H H 7.896 0.01 1 32 . 9 PHE HA H 4.267 0.01 1 33 . 9 PHE HB3 H 2.872 0.01 2 34 . 9 PHE HB2 H 2.729 0.01 2 35 . 9 PHE HD1 H 7.046 0.01 3 36 . 9 PHE HD2 H 6.944 0.01 3 37 . 10 GLY H H 8.203 0.01 1 38 . 10 GLY HA3 H 3.496 0.01 2 39 . 10 GLY HA2 H 3.460 0.01 2 40 . 11 LEU H H 7.682 0.01 1 41 . 11 LEU HA H 3.947 0.01 1 42 . 11 LEU HB3 H 1.147 0.01 2 43 . 11 LEU HB2 H 1.021 0.01 2 44 . 11 LEU HD1 H 0.521 0.01 1 45 . 12 PHE H H 8.058 0.01 1 46 . 12 PHE HA H 4.389 0.01 1 47 . 12 PHE HB3 H 2.957 0.01 2 48 . 12 PHE HB2 H 2.627 0.01 2 49 . 12 PHE HD1 H 7.010 0.01 3 50 . 12 PHE HD2 H 6.945 0.01 3 51 . 13 ASP H H 7.741 0.01 1 52 . 13 ASP HA H 4.142 0.01 1 53 . 13 ASP HB3 H 2.444 0.01 2 54 . 13 ASP HB2 H 2.419 0.01 2 stop_ save_