data_5410 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of novel non-RGD containing short disintegrin by high resolution NMR ; _BMRB_accession_number 5410 _BMRB_flat_file_name bmr5410.str _Entry_type original _Submission_date 2002-07-03 _Accession_date 2002-07-03 _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 Moreno-Murciano Paz . . 2 Monleon Daniel . . 3 Calvete 'Juan J.' . . 4 Celda Bernardo . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 198 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2003-02-18 original BMRB . stop_ _Original_release_date 2002-07-03 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Amino Acid Sequence and Homology Modeling of Obtustatin, a Novel non-RGD-containing short Disintegrin isolated from the Venom of Vipera lebetina obtusa ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 12538900 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Moreno-Murciano Paz . . 2 Monleon Daniel . . 3 Calvete 'Juan J.' . . 4 Celda Bernardo . . 5 Marcinkiewicz C. . . stop_ _Journal_abbreviation 'Protein Sci.' _Journal_volume 12 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 366 _Page_last 371 _Year 2003 _Details . loop_ _Keyword NMR 'disintegrin obtustatin' 'non-RGD integrin antagonist' stop_ save_ ################################## # Molecular system description # ################################## save_system_obtustatin _Saveframe_category molecular_system _Mol_system_name obtustatin _Abbreviation_common obtustatin _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label obtustatin $obtustatin 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_obtustatin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common obtustatin _Abbreviation_common obtustatin _Molecular_mass . _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 41 _Mol_residue_sequence ; CTTGPCCRQCKLKPAGTTCW KTSLTSHYCTGKSCDCPLYP G ; loop_ _Residue_seq_code _Residue_label 1 CYS 2 THR 3 THR 4 GLY 5 PRO 6 CYS 7 CYS 8 ARG 9 GLN 10 CYS 11 LYS 12 LEU 13 LYS 14 PRO 15 ALA 16 GLY 17 THR 18 THR 19 CYS 20 TRP 21 LYS 22 THR 23 SER 24 LEU 25 THR 26 SER 27 HIS 28 TYR 29 CYS 30 THR 31 GLY 32 LYS 33 SER 34 CYS 35 ASP 36 CYS 37 PRO 38 LEU 39 TYR 40 PRO 41 GLY 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 PDB 1MPZ 'Nmr Solution Structure Of Native Viperidae Lebetina Obtusa Protein' 97.56 41 100.00 100.00 5.16e-14 SWISS-PROT P83469 'Short disintegrin obtustatin' 100.00 41 100.00 100.00 1.73e-14 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $obtustatin 'lebetina obtusa' 8703 Eukaryota Metazoa Vipera 'lebetina obtusa' 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 $obtustatin '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 _Concentration_min_value _Concentration_max_value _Isotopic_labeling $obtustatin 1.1 mM 0.8 1.3 . stop_ save_ ############################ # Computer software used # ############################ save_xwinnmr _Saveframe_category software _Name xwinnmr _Version 3.1 loop_ _Task 'spectral processing' stop_ _Details . save_ save_sparky _Saveframe_category software _Name SPARKY _Version 3.96 loop_ _Task 'spectral analysis' stop_ _Details 'Goddard, T. UCSF.' save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AVANCEDMX _Field_strength 500 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AVANCEDMX _Field_strength 600 _Details . save_ save_NMR_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AVANCEDMX _Field_strength 800 _Details . save_ ############################# # NMR applied experiments # ############################# save_mixing_time_TOCSYs_15,50_and_80_ms_1 _Saveframe_category NMR_applied_experiment _Experiment_name 'mixing time TOCSYs 15,50 and 80 ms' _Sample_label $Sample_1 save_ save_mixing_time_NOESYs_50,_100_and_200_ms_2 _Saveframe_category NMR_applied_experiment _Experiment_name 'mixing time NOESYs 50, 100 and 200 ms' _Sample_label $Sample_1 save_ ####################### # Sample conditions # ####################### save_Cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH* 2.5 0.5 n/a temperature 298 0.2 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 0.0 internal direct . . . 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_shifts _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label 'mixing time TOCSYs 15,50 and 80 ms' 'mixing time NOESYs 50, 100 and 200 ms' stop_ loop_ _Sample_label $Sample_1 stop_ _Sample_conditions_label $Cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name obtustatin _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 CYS H H 7.289 0.01 1 2 . 1 CYS HA H 4.368 0.01 1 3 . 1 CYS HB2 H 2.686 0.01 1 4 . 1 CYS HB3 H 2.686 0.01 1 5 . 2 THR H H 8.476 0.01 1 6 . 2 THR HA H 4.163 0.01 1 7 . 2 THR HB H 3.874 0.01 1 8 . 2 THR HG2 H 1.087 0.01 1 9 . 3 THR H H 8.166 0.01 1 10 . 3 THR HA H 4.503 0.01 1 11 . 3 THR HB H 4.025 0.01 1 12 . 3 THR HG2 H 1.023 0.01 1 13 . 4 GLY H H 8.103 0.01 1 14 . 4 GLY HA2 H 3.938 0.01 2 15 . 4 GLY HA3 H 4.119 0.01 2 16 . 5 PRO HA H 4.459 0.01 1 17 . 5 PRO HB2 H 1.799 0.01 2 18 . 5 PRO HB3 H 2.466 0.01 2 19 . 5 PRO HG2 H 1.853 0.01 2 20 . 5 PRO HG3 H 2.074 0.01 2 21 . 5 PRO HD2 H 3.725 0.01 2 22 . 5 PRO HD3 H 3.591 0.01 2 23 . 6 CYS H H 8.519 0.01 1 24 . 6 CYS HA H 4.681 0.01 1 25 . 6 CYS HB2 H 2.423 0.01 2 26 . 6 CYS HB3 H 3.733 0.01 2 27 . 7 CYS H H 8.170 0.01 1 28 . 7 CYS HA H 4.970 0.01 1 29 . 7 CYS HB2 H 2.305 0.01 2 30 . 7 CYS HB3 H 3.290 0.01 2 31 . 8 ARG H H 8.857 0.01 1 32 . 8 ARG HA H 4.417 0.01 1 33 . 8 ARG HD2 H 3.057 0.01 1 34 . 8 ARG HD3 H 3.057 0.01 1 35 . 8 ARG HG2 H 1.281 0.01 1 36 . 8 ARG HG3 H 1.281 0.01 1 37 . 8 ARG HB2 H 1.463 0.01 2 38 . 8 ARG HB3 H 1.604 0.01 2 39 . 9 GLN H H 7.011 0.01 1 40 . 9 GLN HA H 4.483 0.01 1 41 . 9 GLN HB2 H 3.863 0.01 2 42 . 9 GLN HB3 H 3.533 0.01 2 43 . 9 GLN HG2 H 3.042 0.01 1 44 . 9 GLN HG3 H 3.042 0.01 1 45 . 10 CYS H H 8.976 0.01 1 46 . 10 CYS HA H 4.332 0.01 1 47 . 10 CYS HB2 H 2.685 0.01 2 48 . 10 CYS HB3 H 2.470 0.01 2 49 . 11 LYS H H 7.886 0.01 1 50 . 11 LYS HA H 4.428 0.01 1 51 . 11 LYS HB2 H 1.689 0.01 1 52 . 11 LYS HB3 H 1.689 0.01 1 53 . 11 LYS HD2 H 1.527 0.01 1 54 . 11 LYS HD3 H 1.527 0.01 1 55 . 11 LYS HG2 H 1.262 0.01 2 56 . 11 LYS HG3 H 1.330 0.01 2 57 . 12 LEU H H 8.417 0.01 1 58 . 12 LEU HA H 4.079 0.01 1 59 . 12 LEU HG H 0.966 0.01 1 60 . 12 LEU HB2 H 1.415 0.01 1 61 . 12 LEU HB3 H 1.415 0.01 1 62 . 13 LYS H H 8.532 0.01 1 63 . 13 LYS HA H 4.291 0.01 1 64 . 13 LYS HB2 H 1.541 0.01 1 65 . 13 LYS HB3 H 1.541 0.01 1 66 . 13 LYS HD2 H 0.893 0.01 2 67 . 13 LYS HD3 H 1.622 0.01 2 68 . 13 LYS HG2 H 1.252 0.01 1 69 . 13 LYS HG3 H 1.252 0.01 1 70 . 14 PRO HA H 4.254 0.01 1 71 . 14 PRO HB2 H 2.199 0.01 1 72 . 14 PRO HB3 H 2.199 0.01 1 73 . 14 PRO HG2 H 1.673 0.01 2 74 . 14 PRO HG3 H 1.783 0.01 2 75 . 14 PRO HD2 H 3.368 0.01 2 76 . 14 PRO HD3 H 3.637 0.01 2 77 . 15 ALA H H 8.715 0.01 1 78 . 15 ALA HA H 3.717 0.01 1 79 . 15 ALA HB H 1.128 0.01 1 80 . 16 GLY H H 8.238 0.01 1 81 . 16 GLY HA2 H 3.269 0.01 2 82 . 16 GLY HA3 H 4.148 0.01 2 83 . 17 THR H H 7.355 0.01 1 84 . 17 THR HA H 4.049 0.01 1 85 . 17 THR HB H 3.591 0.01 1 86 . 17 THR HG2 H 1.173 0.01 1 87 . 18 THR H H 9.031 0.01 1 88 . 18 THR HA H 4.172 0.01 1 89 . 18 THR HB H 3.967 0.01 1 90 . 18 THR HG2 H 1.026 0.01 1 91 . 19 CYS H H 8.884 0.01 1 92 . 19 CYS HA H 4.793 0.01 1 93 . 19 CYS HB2 H 2.946 0.01 2 94 . 19 CYS HB3 H 2.711 0.01 2 95 . 20 TRP H H 7.737 0.01 1 96 . 20 TRP HA H 4.509 0.01 1 97 . 20 TRP HB2 H 2.608 0.01 2 98 . 20 TRP HB3 H 3.224 0.01 2 99 . 21 LYS H H 7.986 0.01 1 100 . 21 LYS HA H 4.535 0.01 1 101 . 21 LYS HB2 H 1.110 0.01 2 102 . 21 LYS HB3 H 1.484 0.01 2 103 . 21 LYS HD2 H 1.050 0.01 1 104 . 21 LYS HD3 H 1.050 0.01 1 105 . 21 LYS HG2 H 1.423 0.01 1 106 . 21 LYS HG3 H 1.423 0.01 1 107 . 22 THR H H 8.187 0.01 1 108 . 22 THR HA H 4.313 0.01 1 109 . 22 THR HG2 H 0.767 0.01 1 110 . 23 SER H H 8.407 0.01 1 111 . 23 SER HA H 4.024 0.01 1 112 . 23 SER HB2 H 3.773 0.01 1 113 . 23 SER HB3 H 3.773 0.01 1 114 . 24 LEU H H 7.799 0.01 1 115 . 24 LEU HA H 4.302 0.01 1 116 . 24 LEU HG H 0.719 0.01 1 117 . 24 LEU HB2 H 1.463 0.01 1 118 . 24 LEU HB3 H 1.463 0.01 1 119 . 24 LEU HD1 H 0.279 0.01 1 120 . 24 LEU HD2 H 0.279 0.01 1 121 . 25 THR H H 7.386 0.01 1 122 . 25 THR HA H 4.431 0.01 1 123 . 25 THR HB H 3.870 0.01 1 124 . 25 THR HG2 H 0.884 0.01 1 125 . 26 SER H H 8.080 0.01 1 126 . 26 SER HA H 4.810 0.01 1 127 . 26 SER HB2 H 3.429 0.01 2 128 . 26 SER HB3 H 3.290 0.01 2 129 . 27 HIS H H 8.556 0.01 1 130 . 27 HIS HA H 4.713 0.01 1 131 . 27 HIS HB2 H 2.966 0.01 2 132 . 27 HIS HB3 H 2.810 0.01 2 133 . 28 TYR H H 8.435 0.01 1 134 . 28 TYR HA H 5.171 0.01 1 135 . 28 TYR HB2 H 2.584 0.01 2 136 . 28 TYR HB3 H 2.516 0.01 2 137 . 28 TYR HD1 H 6.801 0.01 1 138 . 28 TYR HD2 H 6.801 0.01 1 139 . 28 TYR HE1 H 6.608 0.01 1 140 . 28 TYR HE2 H 6.608 0.01 1 141 . 29 CYS H H 9.292 0.01 1 142 . 29 CYS HA H 4.750 0.01 1 143 . 29 CYS HB2 H 2.473 0.01 2 144 . 29 CYS HB3 H 3.769 0.01 2 145 . 30 THR H H 9.845 0.01 1 146 . 30 THR HA H 4.342 0.01 1 147 . 31 GLY H H 8.208 0.01 1 148 . 31 GLY HA2 H 4.060 0.01 2 149 . 31 GLY HA3 H 4.233 0.01 2 150 . 32 LYS H H 7.931 0.01 1 151 . 32 LYS HA H 4.417 0.01 1 152 . 32 LYS HB2 H 1.846 0.01 1 153 . 32 LYS HB3 H 1.846 0.01 1 154 . 32 LYS HD2 H 1.168 0.01 1 155 . 32 LYS HD3 H 1.168 0.01 1 156 . 32 LYS HG2 H 1.448 0.01 1 157 . 32 LYS HG3 H 1.448 0.01 1 158 . 33 SER H H 8.023 0.01 1 159 . 33 SER HA H 4.817 0.01 1 160 . 33 SER HB2 H 3.422 0.01 2 161 . 33 SER HB3 H 3.285 0.01 2 162 . 34 CYS H H 8.449 0.01 1 163 . 34 CYS HA H 4.443 0.01 1 164 . 34 CYS HB2 H 2.389 0.01 2 165 . 34 CYS HB3 H 2.480 0.01 2 166 . 35 ASP H H 8.768 0.01 1 167 . 35 ASP HA H 5.182 0.01 1 168 . 35 ASP HB2 H 2.483 0.01 2 169 . 35 ASP HB3 H 2.758 0.01 2 170 . 36 CYS H H 8.915 0.01 1 171 . 36 CYS HA H 4.808 0.01 1 172 . 36 CYS HB2 H 2.961 0.01 2 173 . 36 CYS HB3 H 2.729 0.01 2 174 . 37 PRO HA H 4.162 0.01 1 175 . 37 PRO HB2 H 1.928 0.01 2 176 . 37 PRO HB3 H 1.676 0.01 2 177 . 37 PRO HG2 H 1.706 0.01 2 178 . 37 PRO HG3 H 2.050 0.01 2 179 . 37 PRO HD2 H 3.414 0.01 2 180 . 37 PRO HD3 H 3.771 0.01 2 181 . 38 LEU H H 7.789 0.01 1 182 . 38 LEU HA H 3.275 0.01 1 183 . 38 LEU HG H 0.594 0.01 1 184 . 38 LEU HB2 H 1.314 0.01 1 185 . 38 LEU HB3 H 1.314 0.01 1 186 . 38 LEU HD1 H 0.291 0.01 2 187 . 38 LEU HD2 H 0.367 0.01 2 188 . 39 TYR H H 7.359 0.01 1 189 . 39 TYR HA H 4.706 0.01 1 190 . 39 TYR HB2 H 2.908 0.01 2 191 . 39 TYR HB3 H 2.635 0.01 2 192 . 40 PRO HA H 4.211 0.01 1 193 . 40 PRO HB2 H 2.056 0.01 1 194 . 40 PRO HB3 H 2.056 0.01 1 195 . 40 PRO HG2 H 1.853 0.01 1 196 . 40 PRO HG3 H 1.853 0.01 1 197 . 40 PRO HD2 H 3.480 0.01 2 198 . 40 PRO HD3 H 3.591 0.01 2 stop_ save_