data_25190 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Protection against experimental P. falciparum malaria is associated with short AMA-1 peptide analogue alpha-helical structures ; _BMRB_accession_number 25190 _BMRB_flat_file_name bmr25190.str _Entry_type original _Submission_date 2014-09-01 _Accession_date 2014-09-01 _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 Cubillos Marcia . . 2 Salazar 'Luz Mary' . . 3 Torres Libardo . . 4 Patarroyo 'Manuel Elkin' . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 118 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2015-10-01 update BMRB 'update entry citation' 2014-10-07 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 25189 'malaria peptide 1815' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Protection against experimental P. falciparum malaria is associated with short AMA-1 peptide analogue alpha-helical structures ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 12628294 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Cubillos Marcia . . 2 Salazar 'Luz Mary' . . 3 Torres Libardo . . 4 Patarroyo 'Manuel Elkin' . . stop_ _Journal_abbreviation Biochemie _Journal_volume 84 _Journal_issue 12 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1181 _Page_last 1188 _Year 2002 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'malaria short AMA-1 peptide analogue' _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 2271.702 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 21 _Mol_residue_sequence ; MIKSAFLPTGAFKADRYKSH X ; loop_ _Residue_seq_code _Residue_label 1 MET 2 ILE 3 LYS 4 SER 5 ALA 6 PHE 7 LEU 8 PRO 9 THR 10 GLY 11 ALA 12 PHE 13 LYS 14 ALA 15 ASP 16 ARG 17 TYR 18 LYS 19 SER 20 HIS 21 NH2 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 1YXE "Structure And Inter-Domain Interactions Of Domain Ii From The Blood Stage Malarial Protein, Apical Membrane Antigen 1" 95.24 140 100.00 100.00 4.12e-04 PDB 1Z40 "Ama1 From Plasmodium Falciparum" 95.24 336 100.00 100.00 5.12e-04 PDB 2J5L "Structure Of A Plasmodium Falciparum Apical Membrane Antigen 1-Fab F8.12.19 Complex" 95.24 581 100.00 100.00 6.40e-04 PDB 2MTX "Protection Against Experimental P. Falciparum Malaria Is Associated With Short Ama-1 Peptide Analogue Alpha-helical Structures" 95.24 21 100.00 100.00 2.08e-04 PDB 2Q8A "Structure Of The Malaria Antigen Ama1 In Complex With A Growth- Inhibitory Antibody" 95.24 336 100.00 100.00 5.12e-04 PDB 2Q8B "Structure Of The Malaria Antigen Ama1 In Complex With A Growth- Inhibitory Antibody" 95.24 336 100.00 100.00 5.12e-04 PDB 2Z8V "Structure Of An Ignar-Ama1 Complex" 95.24 335 100.00 100.00 5.16e-04 PDB 2Z8W "Structure Of An Ignar-Ama1 Complex" 95.24 335 100.00 100.00 5.16e-04 PDB 3SRI "Crystal Structure Of Plasmodium Falciparum Ama1 In Complex With A 29aa Pfron2 Peptide" 95.24 381 100.00 100.00 8.51e-04 PDB 3SRJ "Pfama1 In Complex With Invasion-Inhibitory Peptide R1" 95.24 381 100.00 100.00 8.51e-04 PDB 3ZWZ "Crystal Structure Of Plasmodium Falciparum Ama1 In Complex With A 39aa Pfron2 Peptide" 95.24 347 100.00 100.00 6.56e-04 PDB 4R19 "Crystal Structure Of 3d7 Strain Plasmodium Falciparum Ama1" 95.24 335 100.00 100.00 5.16e-04 PDB 4R1A "Crystal Structure Of Fvo Strain Plasmodium Falciparum Ama1" 95.24 335 100.00 100.00 3.38e-04 PDB 4R1B "Crystal Structure Of 3d7 Strain Plasmodium Falciparum Ama1" 95.24 335 100.00 100.00 5.16e-04 PDB 4R1C "Crystal Structure Of 3d7 Strain Plasmodium Falciparum Ama1" 95.24 335 100.00 100.00 5.16e-04 DBJ BAM85358 "apical membrane antigen 1 [Plasmodium falciparum]" 95.24 622 100.00 100.00 7.90e-04 DBJ BAM85359 "apical membrane antigen 1 [Plasmodium falciparum]" 90.48 622 100.00 100.00 5.89e-03 DBJ BAM85360 "apical membrane antigen 1 [Plasmodium falciparum]" 95.24 622 100.00 100.00 9.21e-04 DBJ BAM85361 "apical membrane antigen 1 [Plasmodium falciparum]" 95.24 622 100.00 100.00 9.47e-04 DBJ BAM85362 "apical membrane antigen 1 [Plasmodium falciparum]" 90.48 622 100.00 100.00 6.80e-03 EMBL CAB66387 "apical membrane antigen 1, partial [Plasmodium reichenowi]" 95.24 605 100.00 100.00 6.09e-04 EMBL CAB97180 "apical membrane antigen 1, partial [Plasmodium falciparum]" 90.48 526 100.00 100.00 4.86e-03 EMBL CAB97181 "apical membrane antigen 1, partial [Plasmodium falciparum]" 95.24 526 100.00 100.00 4.49e-04 EMBL CAB97183 "apical membrane antigen 1, partial [Plasmodium falciparum]" 95.24 526 100.00 100.00 5.44e-04 EMBL CAB97184 "apical membrane antigen 1, partial [Plasmodium falciparum]" 95.24 526 100.00 100.00 5.18e-04 GB AAA29475 "apical membrane antigen 1 [Plasmodium falciparum]" 95.24 622 100.00 100.00 8.77e-04 GB AAA29476 "apical membrane antigen 1, partial [Plasmodium falciparum]" 95.24 463 100.00 100.00 1.08e-03 GB AAA29718 "merozoite surface antigen [Plasmodium falciparum]" 95.24 622 100.00 100.00 7.60e-04 GB AAA29719 "merozoite surface antigen [Plasmodium falciparum]" 95.24 622 100.00 100.00 7.60e-04 GB AAA29720 "merozoite surface antigen [Plasmodium falciparum]" 90.48 622 100.00 100.00 6.12e-03 REF XP_001348015 "apical membrane antigen 1, AMA1 [Plasmodium falciparum 3D7]" 95.24 622 100.00 100.00 7.67e-04 REF XP_012763735 "apical membrane antigen 1 [Plasmodium reichenowi]" 95.24 622 100.00 100.00 6.15e-04 SP P22621 "RecName: Full=Apical membrane antigen 1; AltName: Full=Merozoite surface antigen; Flags: Precursor" 95.24 622 100.00 100.00 8.77e-04 SP P50489 "RecName: Full=Apical membrane antigen 1; AltName: Full=Merozoite surface antigen; Flags: Precursor" 95.24 622 100.00 100.00 7.60e-04 SP P50490 "RecName: Full=Apical membrane antigen 1; AltName: Full=Merozoite surface antigen; Flags: Precursor" 95.24 622 100.00 100.00 7.60e-04 SP P50491 "RecName: Full=Apical membrane antigen 1; AltName: Full=Merozoite surface antigen; Flags: Precursor" 90.48 622 100.00 100.00 6.12e-03 SP P50492 "RecName: Full=Apical membrane antigen 1; AltName: Full=Merozoite surface antigen; Flags: Precursor" 90.48 622 100.00 100.00 8.72e-03 stop_ save_ ###################### # Polymer residues # ###################### save_chem_comp_NH2 _Saveframe_category polymer_residue _Mol_type NON-POLYMER _Name_common 'AMINO GROUP' _BMRB_code NH2 _PDB_code NH2 _Standard_residue_derivative . _Molecular_mass 16.023 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? HN1 HN1 H . 0 . ? HN2 HN2 H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING N HN1 ? ? SING N HN2 ? ? 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 _Isotopic_labeling $entity 8 mM '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 500 _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 pH 3.7 . pH pressure 1 . atm temperature 295 . 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 DSS C 13 'methyl protons' ppm 0.00 na indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 DSS N 15 'methyl protons' ppm 0.00 na indirect . . . 0.101329118 DSS P 31 'methyl protons' ppm 0.00 na indirect . . . 0.404808636 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' 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 MET H H 8.420 0.02 1 2 1 1 MET HA H 4.040 0.02 1 3 1 1 MET HB2 H 2.040 0.02 1 4 1 1 MET HB3 H 2.040 0.02 1 5 1 1 MET HG2 H 2.460 0.02 1 6 1 1 MET HG3 H 2.460 0.02 1 7 2 2 ILE H H 8.460 0.02 1 8 2 2 ILE HA H 4.120 0.02 1 9 2 2 ILE HB H 1.740 0.02 1 10 2 2 ILE HG12 H 1.390 0.02 1 11 2 2 ILE HG13 H 1.390 0.02 1 12 2 2 ILE HG2 H 0.810 0.02 1 13 2 2 ILE HD1 H 0.760 0.02 1 14 3 3 LYS H H 8.360 0.02 1 15 3 3 LYS HA H 4.220 0.02 1 16 3 3 LYS HB2 H 1.730 0.02 2 17 3 3 LYS HB3 H 1.630 0.02 2 18 3 3 LYS HG2 H 1.320 0.02 1 19 3 3 LYS HG3 H 1.320 0.02 1 20 3 3 LYS HD2 H 1.580 0.02 1 21 3 3 LYS HD3 H 1.580 0.02 1 22 3 3 LYS HE2 H 2.880 0.02 1 23 3 3 LYS HE3 H 2.880 0.02 1 24 4 4 SER H H 8.100 0.02 1 25 4 4 SER HA H 4.270 0.02 1 26 4 4 SER HB2 H 3.730 0.02 2 27 4 4 SER HB3 H 3.650 0.02 2 28 5 5 ALA H H 8.180 0.02 1 29 5 5 ALA HA H 4.160 0.02 1 30 5 5 ALA HB H 1.140 0.02 1 31 6 6 PHE H H 7.920 0.02 1 32 6 6 PHE HA H 4.500 0.02 1 33 6 6 PHE HB2 H 2.990 0.02 2 34 6 6 PHE HB3 H 2.860 0.02 2 35 6 6 PHE HE1 H 7.110 0.02 1 36 6 6 PHE HE2 H 7.110 0.02 1 37 7 7 LEU H H 7.830 0.02 1 38 7 7 LEU HA H 4.510 0.02 1 39 7 7 LEU HB2 H 1.460 0.02 1 40 7 7 LEU HB3 H 1.460 0.02 1 41 7 7 LEU HG H 1.370 0.02 1 42 7 7 LEU HD1 H 0.780 0.02 1 43 7 7 LEU HD2 H 0.780 0.02 1 44 8 8 PRO HA H 4.340 0.02 1 45 8 8 PRO HB2 H 2.170 0.02 2 46 8 8 PRO HB3 H 1.880 0.02 2 47 8 8 PRO HD2 H 3.600 0.02 2 48 8 8 PRO HD3 H 3.460 0.02 2 49 9 9 THR H H 7.960 0.02 1 50 9 9 THR HA H 4.140 0.02 1 51 9 9 THR HG2 H 1.260 0.02 1 52 10 10 GLY H H 8.300 0.02 1 53 10 10 GLY HA2 H 3.820 0.02 1 54 10 10 GLY HA3 H 3.820 0.02 1 55 11 11 ALA H H 7.940 0.02 1 56 11 11 ALA HA H 4.110 0.02 1 57 11 11 ALA HB H 1.170 0.02 1 58 12 12 PHE H H 7.950 0.02 1 59 12 12 PHE HA H 4.410 0.02 1 60 12 12 PHE HB2 H 2.950 0.02 1 61 12 12 PHE HB3 H 2.950 0.02 1 62 12 12 PHE HE1 H 7.120 0.02 1 63 12 12 PHE HE2 H 7.120 0.02 1 64 13 13 LYS H H 7.910 0.02 1 65 13 13 LYS HA H 4.040 0.02 1 66 13 13 LYS HB2 H 1.670 0.02 2 67 13 13 LYS HB3 H 1.590 0.02 2 68 13 13 LYS HG2 H 1.250 0.02 1 69 13 13 LYS HG3 H 1.250 0.02 1 70 13 13 LYS HD2 H 1.550 0.02 1 71 13 13 LYS HD3 H 1.550 0.02 1 72 13 13 LYS HE2 H 2.860 0.02 1 73 13 13 LYS HE3 H 2.860 0.02 1 74 14 14 ALA H H 7.800 0.02 1 75 14 14 ALA HA H 4.090 0.02 1 76 14 14 ALA HB H 1.280 0.02 1 77 15 15 ASP H H 8.150 0.02 1 78 15 15 ASP HA H 4.500 0.02 1 79 15 15 ASP HB2 H 2.720 0.02 1 80 15 15 ASP HB3 H 2.720 0.02 1 81 16 16 ARG H H 7.960 0.02 1 82 16 16 ARG HA H 4.050 0.02 1 83 16 16 ARG HB2 H 1.760 0.02 1 84 16 16 ARG HB3 H 1.760 0.02 1 85 16 16 ARG HG2 H 1.540 0.02 2 86 16 16 ARG HG3 H 1.260 0.02 2 87 16 16 ARG HD2 H 2.950 0.02 1 88 16 16 ARG HD3 H 2.950 0.02 1 89 16 16 ARG HH11 H 6.980 0.02 1 90 16 16 ARG HH12 H 6.980 0.02 1 91 16 16 ARG HH21 H 6.980 0.02 1 92 16 16 ARG HH22 H 6.980 0.02 1 93 17 17 TYR H H 7.860 0.02 1 94 17 17 TYR HA H 4.140 0.02 1 95 17 17 TYR HB2 H 3.000 0.02 2 96 17 17 TYR HB3 H 2.810 0.02 2 97 17 17 TYR HD1 H 7.020 0.02 1 98 17 17 TYR HD2 H 7.020 0.02 1 99 17 17 TYR HE1 H 6.690 0.02 1 100 17 17 TYR HE2 H 6.690 0.02 1 101 18 18 LYS H H 7.230 0.02 1 102 18 18 LYS HA H 4.160 0.02 1 103 18 18 LYS HB2 H 1.700 0.02 2 104 18 18 LYS HB3 H 1.610 0.02 2 105 18 18 LYS HG2 H 1.260 0.02 1 106 18 18 LYS HG3 H 1.260 0.02 1 107 18 18 LYS HD2 H 1.560 0.02 1 108 18 18 LYS HD3 H 1.560 0.02 1 109 18 18 LYS HE2 H 2.870 0.02 1 110 18 18 LYS HE3 H 2.870 0.02 1 111 19 19 SER H H 8.080 0.02 1 112 19 19 SER HA H 4.230 0.02 1 113 19 19 SER HB2 H 3.770 0.02 2 114 19 19 SER HB3 H 3.700 0.02 2 115 20 20 HIS H H 8.360 0.02 1 116 20 20 HIS HA H 4.570 0.02 1 117 20 20 HIS HB2 H 3.200 0.02 2 118 20 20 HIS HB3 H 3.060 0.02 2 stop_ save_