data_5114 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Refined Structure and Metal Binding site of the Kalata B1 Peptide ; _BMRB_accession_number 5114 _BMRB_flat_file_name bmr5114.str _Entry_type original _Submission_date 2001-08-15 _Accession_date 2001-08-15 _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 Skjeldal L. . . 2 Gran L. . . 3 Sletten K. . . 4 Volkman B. F. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 143 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2002-04-08 original BMRB . stop_ _Original_release_date 2001-08-15 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Refined Structure and Metal Binding Site of the Kalata B1 Peptide ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 21885728 _PubMed_ID 11888199 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Skjeldal L. . . 2 Gran L. . . 3 Sletten K. . . 4 Volkman B. F. . stop_ _Journal_abbreviation 'Arch. Biochem. Biophys.' _Journal_volume 399 _Journal_issue 2 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 142 _Page_last 148 _Year 2002 _Details . loop_ _Keyword 'cyclic peptide' cyclotide 'disulfide pairing' uterotonic stop_ save_ ################################## # Molecular system description # ################################## save_system_kalata_B1 _Saveframe_category molecular_system _Mol_system_name 'KALATA B1' _Abbreviation_common 'kalata B1' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'kalata B1' $kalata_B1 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'all disulfide bound' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_kalata_B1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'kalata B1' _Abbreviation_common 'kalata B1' _Molecular_mass . _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 29 _Mol_residue_sequence ; NGLPVCGETCVGGTCNTPGC TCSWPVCTR ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 8 ASN 2 9 GLY 3 10 LEU 4 11 PRO 5 12 VAL 6 13 CYS 7 14 GLY 8 15 GLU 9 16 THR 10 17 CYS 11 18 VAL 12 19 GLY 13 20 GLY 14 21 THR 15 22 CYS 16 23 ASN 17 24 THR 18 25 PRO 19 26 GLY 20 27 CYS 21 28 THR 22 29 CYS 23 30 SER 24 31 TRP 25 32 PRO 26 33 VAL 27 34 CYS 28 35 THR 29 36 ARG stop_ _Sequence_homology_query_date 2008-08-19 _Sequence_homology_query_revised_last_date 2008-08-19 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 BMRB 6627 'Kalata B1' 82.76 29 100.00 100.00 2.11e-04 PDB 1JJZ 'Refined Structure And Disulfide Pairing Of The Kalata B1 Peptide' 93.10 29 100.00 100.00 7.69e-06 PDB 1K48 'Refined Structure And Disulfide Pairing Of The Kalata B1 Peptide' 93.10 29 100.00 100.00 7.69e-06 PDB 1KAL 'Elucidation Of The Primary And Three-Dimensional Structure Of The Uterotonic Polypeptide Kalata B1' 75.86 29 100.00 100.00 8.29e-03 PDB 1NB1 'High Resolution Solution Structure Of Kalata B1' 82.76 29 100.00 100.00 2.11e-04 PDB 1ORX 'Solution Structure Of The Acyclic Permutant Des-(24-28)- Kalata B1' 79.31 24 100.00 100.00 1.30e-03 PDB 1ZNU 'Structure Of Cyclotide Kalata B1 In Dpc Micelles Solution' 79.31 29 100.00 100.00 6.84e-04 PIR A56283 'kalata B1 [validated] - Oldenlandia affinis' 75.86 29 100.00 100.00 7.20e-03 SWISS-PROT P83938 Kalata-B4 96.55 29 100.00 100.00 1.22e-06 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $kalata_B1 'Oldenlandia affinis' 60225 Eukaryota Viridiplantae Oldenlandia affinis 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 $kalata_B1 'purified from the natural source' . . . . . 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 $kalata_B1 5 mM . H2O 90 % . D2O 10 % . stop_ save_ ############################ # Computer software used # ############################ save_DYANA _Saveframe_category software _Name DYANA _Version 1.5 loop_ _Task refinement stop_ _Details 'P. Guentert' save_ save_XWINNMR _Saveframe_category software _Name xwinnmr _Version 2.6 loop_ _Task collection stop_ _Details Bruker save_ save_Xeasy _Saveframe_category software _Name XEASY _Version 1.3.11 loop_ _Task 'data analysis' stop_ _Details 'C. Bartels' save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DMX _Field_strength 750 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label . save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 3 . n/a pressure 1 . atm temperature 298 . K 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 DSS H 1 'methyl protons' ppm 0.00 internal . . . . 1.0 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_ _Experiment_label '2D NOESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'kalata B1' _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 8 1 ASN H H 9.52 0.02 1 2 8 1 ASN HA H 4.36 0.02 1 3 8 1 ASN HB2 H 3.06 0.02 2 4 8 1 ASN HB3 H 2.80 0.02 2 5 8 1 ASN HD21 H 7.57 0.02 2 6 8 1 ASN HD22 H 6.92 0.02 2 7 9 2 GLY H H 8.72 0.02 1 8 9 2 GLY HA2 H 4.20 0.02 2 9 9 2 GLY HA3 H 3.56 0.02 2 10 10 3 LEU H H 7.72 0.02 1 11 10 3 LEU HA H 5.02 0.02 1 12 10 3 LEU HB2 H 1.88 0.02 2 13 10 3 LEU HB3 H 1.45 0.02 2 14 10 3 LEU HG H 1.67 0.02 1 15 10 3 LEU HD1 H 0.95 0.02 2 16 10 3 LEU HD2 H 0.88 0.02 2 17 11 4 PRO HA H 5.03 0.02 1 18 11 4 PRO HB2 H 2.42 0.02 2 19 11 4 PRO HB3 H 1.68 0.02 2 20 11 4 PRO HG2 H 2.12 0.02 2 21 11 4 PRO HG3 H 2.01 0.02 2 22 11 4 PRO HD2 H 3.76 0.02 2 23 11 4 PRO HD3 H 3.72 0.02 2 24 12 5 VAL H H 8.10 0.02 1 25 12 5 VAL HA H 4.63 0.02 1 26 12 5 VAL HB H 2.55 0.02 1 27 12 5 VAL HG1 H 0.85 0.02 2 28 12 5 VAL HG2 H 0.80 0.02 2 29 13 6 CYS H H 7.96 0.02 1 30 13 6 CYS HA H 4.44 0.02 1 31 13 6 CYS HB2 H 3.31 0.02 2 32 13 6 CYS HB3 H 2.96 0.02 2 33 14 7 GLY H H 8.49 0.02 1 34 14 7 GLY HA2 H 3.81 0.02 2 35 14 7 GLY HA3 H 3.71 0.02 2 36 15 8 GLU H H 7.14 0.02 1 37 15 8 GLU HA H 4.76 0.02 1 38 15 8 GLU HB2 H 1.98 0.02 2 39 15 8 GLU HB3 H 1.84 0.02 2 40 15 8 GLU HG2 H 2.55 0.02 2 41 15 8 GLU HG3 H 2.49 0.02 2 42 16 9 THR H H 8.43 0.02 1 43 16 9 THR HA H 4.53 0.02 1 44 16 9 THR HB H 4.41 0.02 1 45 16 9 THR HG2 H 1.11 0.02 1 46 17 10 CYS H H 8.31 0.02 1 47 17 10 CYS HA H 4.91 0.02 1 48 17 10 CYS HB2 H 3.15 0.02 2 49 17 10 CYS HB3 H 2.87 0.02 2 50 18 11 VAL H H 8.51 0.02 1 51 18 11 VAL HA H 3.81 0.02 1 52 18 11 VAL HB H 2.00 0.02 1 53 18 11 VAL HG1 H 0.99 0.02 2 54 18 11 VAL HG2 H 0.91 0.02 2 55 19 12 GLY H H 8.65 0.02 1 56 19 12 GLY HA2 H 4.22 0.02 2 57 19 12 GLY HA3 H 3.80 0.02 2 58 20 13 GLY H H 8.18 0.02 1 59 20 13 GLY HA2 H 4.38 0.02 2 60 20 13 GLY HA3 H 4.00 0.02 2 61 21 14 THR H H 7.82 0.02 1 62 21 14 THR HA H 4.06 0.02 1 63 21 14 THR HB H 4.68 0.02 1 64 21 14 THR HG2 H 1.11 0.02 1 65 22 15 CYS H H 8.68 0.02 1 66 22 15 CYS HA H 4.67 0.02 1 67 22 15 CYS HB2 H 3.00 0.02 2 68 22 15 CYS HB3 H 2.73 0.02 2 69 23 16 ASN H H 9.32 0.02 1 70 23 16 ASN HA H 4.67 0.02 1 71 23 16 ASN HB2 H 2.77 0.02 1 72 23 16 ASN HB3 H 2.77 0.02 1 73 23 16 ASN HD21 H 7.61 0.02 2 74 23 16 ASN HD22 H 6.89 0.02 2 75 24 17 THR H H 8.29 0.02 1 76 24 17 THR HA H 4.47 0.02 1 77 24 17 THR HB H 4.17 0.02 1 78 24 17 THR HG2 H 1.30 0.02 1 79 25 18 PRO HA H 4.23 0.02 1 80 25 18 PRO HB2 H 2.29 0.02 2 81 25 18 PRO HB3 H 1.87 0.02 2 82 25 18 PRO HG2 H 2.11 0.02 2 83 25 18 PRO HG3 H 1.97 0.02 2 84 25 18 PRO HD2 H 4.11 0.02 2 85 25 18 PRO HD3 H 3.67 0.02 2 86 26 19 GLY H H 8.75 0.02 1 87 26 19 GLY HA2 H 4.15 0.02 2 88 26 19 GLY HA3 H 3.65 0.02 2 89 27 20 CYS H H 7.66 0.02 1 90 27 20 CYS HA H 5.29 0.02 1 91 27 20 CYS HB2 H 3.78 0.02 2 92 27 20 CYS HB3 H 2.58 0.02 2 93 28 21 THR H H 9.48 0.02 1 94 28 21 THR HA H 4.49 0.02 1 95 28 21 THR HB H 4.00 0.02 1 96 28 21 THR HG2 H 1.09 0.02 1 97 29 22 CYS H H 8.92 0.02 1 98 29 22 CYS HA H 4.56 0.02 1 99 29 22 CYS HB2 H 3.08 0.02 2 100 29 22 CYS HB3 H 2.78 0.02 2 101 30 23 SER H H 8.92 0.02 1 102 30 23 SER HA H 4.74 0.02 1 103 30 23 SER HB2 H 3.81 0.02 1 104 30 23 SER HB3 H 3.81 0.02 1 105 31 24 TRP H H 7.94 0.02 1 106 31 24 TRP HA H 4.02 0.02 1 107 31 24 TRP HB2 H 3.21 0.02 1 108 31 24 TRP HB3 H 3.21 0.02 1 109 31 24 TRP HD1 H 7.26 0.02 1 110 31 24 TRP HE3 H 7.39 0.02 1 111 31 24 TRP HE1 H 10.38 0.02 1 112 31 24 TRP HZ3 H 7.07 0.02 1 113 31 24 TRP HZ2 H 7.47 0.02 1 114 31 24 TRP HH2 H 7.16 0.02 1 115 32 25 PRO HA H 3.38 0.02 1 116 32 25 PRO HB2 H 1.64 0.02 2 117 32 25 PRO HB3 H -0.27 0.02 2 118 32 25 PRO HG2 H 1.31 0.02 2 119 32 25 PRO HG3 H 1.23 0.02 2 120 32 25 PRO HD2 H 3.21 0.02 2 121 32 25 PRO HD3 H 3.16 0.02 2 122 33 26 VAL H H 8.25 0.02 1 123 33 26 VAL HA H 4.18 0.02 1 124 33 26 VAL HB H 1.88 0.02 1 125 33 26 VAL HG1 H 0.81 0.02 2 126 33 26 VAL HG2 H 0.78 0.02 2 127 34 27 CYS H H 7.69 0.02 1 128 34 27 CYS HA H 5.07 0.02 1 129 34 27 CYS HB2 H 3.18 0.02 2 130 34 27 CYS HB3 H 2.71 0.02 2 131 35 28 THR H H 9.83 0.02 1 132 35 28 THR HA H 5.03 0.02 1 133 35 28 THR HB H 3.67 0.02 1 134 35 28 THR HG2 H 0.84 0.02 1 135 36 29 ARG H H 8.67 0.02 1 136 36 29 ARG HA H 4.72 0.02 1 137 36 29 ARG HB2 H 1.64 0.02 2 138 36 29 ARG HB3 H 1.60 0.02 2 139 36 29 ARG HG2 H 1.43 0.02 2 140 36 29 ARG HG3 H 1.39 0.02 2 141 36 29 ARG HD2 H 3.14 0.02 2 142 36 29 ARG HD3 H 3.11 0.02 2 143 36 29 ARG HE H 6.92 0.02 1 stop_ save_