data_25203 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Changing ABRA protein peptide to fit the HLA-DR B1*0301 molecule renders it protection-inducing ; _BMRB_accession_number 25203 _BMRB_flat_file_name bmr25203.str _Entry_type original _Submission_date 2014-09-04 _Accession_date 2014-09-04 _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 Salazar 'Luz M.' . . 2 Alba 'Martha P.' . . 3 Curtidor Hernando . . 4 Bermudez Adriana . . 5 Vargas 'Luis E.' . . 6 Rivera 'Zuly J.' . . 7 Patarroyo 'Manuel E.' . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 128 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-10-07 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 25202 . stop_ _Original_release_date 2014-10-07 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Changing ABRA protein peptide to fit into HLA-DRB1*0301 molecule renders it protection-inducing' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 15313182 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Salazar 'Luz M.' . . 2 Alba 'Martha P.' . . 3 Curtidor Hernando . . 4 Bermudez Adriana . . 5 Vargas 'Luis E.' . . 6 Rivera 'Zuly J.' . . 7 Patarroyo 'Manuel E.' . . stop_ _Journal_abbreviation 'Biochem. Biophys. Res. Commun.' _Journal_volume 322 _Journal_issue 1 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 119 _Page_last 125 _Year 2014 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Peptide of acidic-basic repeat antigen (ABRA) from Plasmodium falciparum' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity $entity stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity _Molecular_mass 2502.966 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 20 _Mol_residue_sequence KMNMLKENVDYIQKNQNLFK loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 LYS 2 2 MET 3 3 ASN 4 4 MET 5 5 LEU 6 6 LYS 7 7 GLU 8 8 ASN 9 9 VAL 10 10 ASP 11 11 TYR 12 12 ILE 13 13 GLN 14 14 LYS 15 15 ASN 16 16 GLN 17 17 ASN 18 18 LEU 19 19 PHE 20 20 LYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-11-25 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 2MU9 "Changing Abra Protein Peptide To Fit The Hla-dr B1*0301 Molecule Renders It Protection-inducing" 100.00 20 100.00 100.00 2.72e-03 EMBL CDO65562 "acidic basic repeat antigen [Plasmodium reichenowi]" 100.00 699 100.00 100.00 1.58e-02 GB AAA29462 "p101/acidic basic repeat antigen [Plasmodium falciparum]" 100.00 743 100.00 100.00 1.63e-02 GB AAF37556 "p101/acidic basic repeat antigen [Plasmodium falciparum]" 100.00 739 100.00 100.00 1.61e-02 GB AAN36363 "Merozoite Surface Protein 9, MSP-9 [Plasmodium falciparum 3D7]" 100.00 743 100.00 100.00 1.63e-02 GB ACR10057 "merozoite surface protein 9, partial [Plasmodium reichenowi]" 100.00 648 100.00 100.00 1.59e-02 GB ACR10058 "merozoite surface protein 9, partial [Plasmodium falciparum]" 100.00 714 100.00 100.00 1.59e-02 REF XP_001350683 "Merozoite Surface Protein 9, MSP-9 [Plasmodium falciparum 3D7]" 100.00 743 100.00 100.00 1.63e-02 REF XP_012764154 "acidic basic repeat antigen [Plasmodium reichenowi]" 100.00 699 100.00 100.00 1.58e-02 SP P22620 "RecName: Full=101 kDa malaria antigen; AltName: Full=Acidic basic repeat antigen; AltName: Full=p101" 100.00 743 100.00 100.00 1.63e-02 SP P23745 "RecName: Full=101 kDa malaria antigen; AltName: Full=Acidic basic repeat antigen; AltName: Full=p101" 100.00 600 100.00 100.00 1.48e-02 SP Q8I5D2 "RecName: Full=101 kDa malaria antigen; AltName: Full=Acidic basic repeat antigen; AltName: Full=p101" 100.00 743 100.00 100.00 1.63e-02 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity 'Malaria parasite' 5833 Eukaryota . Plasmodium falciparum 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 $entity 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details 'trifluoroethanol/water 30%/70%' loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $entity . mM 7 10 'natural abundance' water 70 % . . 'natural abundance' trifluoroethanol 30 % . . 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_InsightII _Saveframe_category software _Name InsightII _Version . loop_ _Vendor _Address _Electronic_address 'Accelrys Software Inc.' . . stop_ loop_ _Task 'geometry optimization' refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_DQF-COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 295 . K pH 3.7 . pH pressure 1 . atm 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 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 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_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H TOCSY' '2D 1H-1H NOESY' 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 entity _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 1 LYS H H 8.200 0.02 1 2 1 1 LYS HA H 4.070 0.02 1 3 1 1 LYS HB2 H 1.790 0.02 1 4 1 1 LYS HB3 H 1.790 0.02 1 5 1 1 LYS HG2 H 1.320 0.02 1 6 1 1 LYS HG3 H 1.320 0.02 1 7 1 1 LYS HD2 H 1.450 0.02 1 8 1 1 LYS HD3 H 1.450 0.02 1 9 2 2 MET H H 8.360 0.02 1 10 2 2 MET HA H 4.310 0.02 1 11 2 2 MET HB2 H 1.990 0.02 1 12 2 2 MET HB3 H 1.990 0.02 1 13 2 2 MET HG2 H 2.460 0.02 1 14 2 2 MET HG3 H 2.460 0.02 1 15 3 3 ASN H H 8.000 0.02 1 16 3 3 ASN HA H 4.450 0.02 1 17 3 3 ASN HB2 H 2.750 0.02 2 18 3 3 ASN HB3 H 2.000 0.02 2 19 3 3 ASN HD21 H 7.520 0.02 2 20 3 3 ASN HD22 H 6.740 0.02 2 21 4 4 MET H H 8.060 0.02 1 22 4 4 MET HA H 4.100 0.02 1 23 4 4 MET HB2 H 2.100 0.02 1 24 4 4 MET HB3 H 2.100 0.02 1 25 4 4 MET HG2 H 2.540 0.02 2 26 4 4 MET HG3 H 2.430 0.02 2 27 5 5 LEU H H 7.890 0.02 1 28 5 5 LEU HA H 4.090 0.02 1 29 5 5 LEU HB2 H 1.630 0.02 1 30 5 5 LEU HB3 H 1.630 0.02 1 31 5 5 LEU HG H 1.570 0.02 1 32 5 5 LEU HD1 H 0.830 0.02 2 33 5 5 LEU HD2 H 0.790 0.02 2 34 6 6 LYS H H 7.910 0.02 1 35 6 6 LYS HA H 3.880 0.02 1 36 6 6 LYS HB2 H 1.790 0.02 1 37 6 6 LYS HB3 H 1.790 0.02 1 38 6 6 LYS HG2 H 1.320 0.02 1 39 6 6 LYS HG3 H 1.320 0.02 1 40 6 6 LYS HD2 H 1.450 0.02 1 41 6 6 LYS HD3 H 1.450 0.02 1 42 7 7 GLU H H 7.890 0.02 1 43 7 7 GLU HA H 4.090 0.02 1 44 7 7 GLU HB2 H 2.060 0.02 1 45 7 7 GLU HB3 H 2.060 0.02 1 46 7 7 GLU HG2 H 2.440 0.02 1 47 7 7 GLU HG3 H 2.440 0.02 1 48 8 8 ASN H H 7.750 0.02 1 49 8 8 ASN HA H 4.550 0.02 1 50 8 8 ASN HB2 H 2.590 0.02 2 51 8 8 ASN HB3 H 2.450 0.02 2 52 8 8 ASN HD21 H 6.900 0.02 2 53 8 8 ASN HD22 H 6.190 0.02 2 54 9 9 VAL H H 8.280 0.02 1 55 9 9 VAL HA H 3.660 0.02 1 56 9 9 VAL HB H 2.070 0.02 1 57 9 9 VAL HG1 H 0.950 0.02 2 58 9 9 VAL HG2 H 0.860 0.02 2 59 10 10 ASP H H 8.300 0.02 1 60 10 10 ASP HA H 4.380 0.02 1 61 10 10 ASP HB2 H 2.850 0.02 2 62 10 10 ASP HB3 H 2.730 0.02 2 63 11 11 TYR H H 7.920 0.02 1 64 11 11 TYR HA H 4.040 0.02 1 65 11 11 TYR HB2 H 3.160 0.02 2 66 11 11 TYR HB3 H 3.100 0.02 2 67 11 11 TYR HD1 H 7.010 0.02 1 68 11 11 TYR HD2 H 7.010 0.02 1 69 11 11 TYR HE1 H 6.530 0.02 1 70 11 11 TYR HE2 H 6.530 0.02 1 71 12 12 ILE H H 8.110 0.02 1 72 12 12 ILE HA H 3.580 0.02 1 73 12 12 ILE HB H 1.890 0.02 1 74 12 12 ILE HG12 H 1.710 0.02 1 75 12 12 ILE HG13 H 1.710 0.02 1 76 12 12 ILE HG2 H 1.040 0.02 1 77 12 12 ILE HD1 H 0.730 0.02 1 78 13 13 GLN H H 8.320 0.02 1 79 13 13 GLN HA H 3.940 0.02 1 80 13 13 GLN HB2 H 2.090 0.02 2 81 13 13 GLN HB3 H 2.020 0.02 2 82 13 13 GLN HG2 H 2.050 0.02 1 83 13 13 GLN HG3 H 2.050 0.02 1 84 14 14 LYS H H 7.910 0.02 1 85 14 14 LYS HA H 4.050 0.02 1 86 14 14 LYS HB2 H 1.780 0.02 2 87 14 14 LYS HB3 H 1.430 0.02 2 88 14 14 LYS HG2 H 1.320 0.02 1 89 14 14 LYS HG3 H 1.320 0.02 1 90 14 14 LYS HD2 H 1.570 0.02 1 91 14 14 LYS HD3 H 1.570 0.02 1 92 15 15 ASN H H 7.750 0.02 1 93 15 15 ASN HA H 4.550 0.02 1 94 15 15 ASN HB2 H 2.590 0.02 2 95 15 15 ASN HB3 H 2.000 0.02 2 96 16 16 GLN H H 8.050 0.02 1 97 16 16 GLN HA H 4.080 0.02 1 98 16 16 GLN HB2 H 2.060 0.02 1 99 16 16 GLN HB3 H 2.060 0.02 1 100 16 16 GLN HG2 H 2.340 0.02 1 101 16 16 GLN HG3 H 2.340 0.02 1 102 17 17 ASN H H 8.210 0.02 1 103 17 17 ASN HA H 4.490 0.02 1 104 17 17 ASN HB2 H 2.700 0.02 1 105 17 17 ASN HB3 H 2.700 0.02 1 106 18 18 LEU H H 7.730 0.02 1 107 18 18 LEU HA H 3.580 0.02 1 108 18 18 LEU HB2 H 1.440 0.02 1 109 18 18 LEU HB3 H 1.440 0.02 1 110 18 18 LEU HG H 1.260 0.02 1 111 18 18 LEU HD1 H 0.770 0.02 2 112 18 18 LEU HD2 H 0.680 0.02 2 113 19 19 PHE H H 7.740 0.02 1 114 19 19 PHE HA H 4.480 0.02 1 115 19 19 PHE HB2 H 3.140 0.02 2 116 19 19 PHE HB3 H 2.920 0.02 2 117 19 19 PHE HD1 H 7.180 0.02 1 118 19 19 PHE HD2 H 7.180 0.02 1 119 19 19 PHE HE1 H 7.250 0.02 1 120 19 19 PHE HE2 H 7.250 0.02 1 121 20 20 LYS H H 7.750 0.02 1 122 20 20 LYS HA H 4.160 0.02 1 123 20 20 LYS HB2 H 1.790 0.02 2 124 20 20 LYS HB3 H 1.680 0.02 2 125 20 20 LYS HG2 H 1.330 0.02 1 126 20 20 LYS HG3 H 1.330 0.02 1 127 20 20 LYS HD2 H 1.380 0.02 1 128 20 20 LYS HD3 H 1.380 0.02 1 stop_ save_