data_4509 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Automated 2D NOESY Assignment and Structure Calculation of crambin(S22/I25) with Self-Correcting Distance Geometry Based NOAH/DIAMOND Programs ; _BMRB_accession_number 4509 _BMRB_flat_file_name bmr4509.str _Entry_type original _Submission_date 1999-10-08 _Accession_date 1999-12-06 _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 Xu Y. . . 2 Wu J. . . 3 Gorenstein D. . . 4 Braun W. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 206 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2000-10-06 original author . stop_ _Original_release_date 2000-10-06 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Automated 2D NOESY assignment and structure calculation of Crambin(S22/I25) with the self-correcting distance geometry based NOAH/DIAMOD programs ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 99106048 _PubMed_ID 9887292 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Xu Y. . . 2 Wu J. . . 3 Gorenstein D. . . 4 Braun W. . . stop_ _Journal_abbreviation 'J. Magn. Reson.' _Journal_volume 136 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 76 _Page_last 85 _Year 1999 _Details . loop_ _Keyword crambin 'crambe abyssinica' 'plant seed protein' stop_ save_ ################################## # Molecular system description # ################################## save_system-crambin _Saveframe_category molecular_system _Mol_system_name crambin _Abbreviation_common crambin _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label crambin $crambin stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'not reported' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_crambin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common crambin _Abbreviation_common crambin _Molecular_mass . _Mol_thiol_state 'not reported' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 46 _Mol_residue_sequence ; TTCCPSIVARSNFNVCRLPG TSEAICATYTGCIIIPGATC PGDYAN ; loop_ _Residue_seq_code _Residue_label 1 THR 2 THR 3 CYS 4 CYS 5 PRO 6 SER 7 ILE 8 VAL 9 ALA 10 ARG 11 SER 12 ASN 13 PHE 14 ASN 15 VAL 16 CYS 17 ARG 18 LEU 19 PRO 20 GLY 21 THR 22 SER 23 GLU 24 ALA 25 ILE 26 CYS 27 ALA 28 THR 29 TYR 30 THR 31 GLY 32 CYS 33 ILE 34 ILE 35 ILE 36 PRO 37 GLY 38 ALA 39 THR 40 CYS 41 PRO 42 GLY 43 ASP 44 TYR 45 ALA 46 ASN stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2014-10-26 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 1541 crambin 100.00 46 97.83 97.83 2.59e-22 BMRB 1542 thionin 100.00 46 97.83 97.83 2.59e-22 PDB 1AB1 "Si Form Crambin" 100.00 46 100.00 100.00 5.22e-23 PDB 1CRN "Water Structure Of A Hydrophobic Protein At Atomic Resolution. Pentagon Rings Of Water Molecules In Crystals Of Crambin" 100.00 46 97.83 97.83 4.08e-22 PDB 1CXR "Automated 2d Noesy Assignment And Structure Calculation Of Crambin(S22I25) WITH SELF-Correcting Distance Geometry Based NoahDIA" 97.83 46 100.00 100.00 2.04e-22 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $crambin 'Abyssinian crambe' 3271 Eukaryota Viridiplantae Crambe abyssinica 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 $crambin . . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details (SER/ILE) loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $crambin 2.5 mM . acetone 75 % [U-2H] H2O 20 % . D2O 5 % . stop_ save_ ############################ # Computer software used # ############################ save_NOAH _Saveframe_category software _Name NOAH _Version 1.0 loop_ _Task 'STRUCTURE SOLUTION' stop_ _Details 'C.MUMENTHALER, Y.XU, W.BRAUN' save_ save_DIAMOD _Saveframe_category software _Name DIAMOD _Version 1.0 loop_ _Task 'STRUCTURE SOLUTION' stop_ _Details 'P. GUNTERT, W. BRAUN, K. WUTHRICH' save_ save_FANTOM _Saveframe_category software _Name FANTOM _Version 4.0 loop_ _Task REFINEMENT stop_ _Details 'TH.SCHAUMANN, W.BRAUN, K.WUTHRICH, R.FRACZKIEWICZ' save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model VXRS _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_1 save_ save_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label $sample_1 save_ save_2D_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label $sample_1 save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.5 . n/a temperature 298 . K pressure 1 . atm stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_shift_ref _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_citation_label _Correction_value_citation_label . H 1 . . . . . . . . $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 $chem_shift_ref _Mol_system_component_name crambin _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 THR HA H 4.225 . . 2 . 1 THR HB H 4.115 . . 3 . 1 THR HG2 H 1.134 . . 4 . 2 THR H H 8.616 . . 5 . 2 THR HA H 5.225 . . 6 . 2 THR HB H 3.731 . . 7 . 2 THR HG2 H 0.869 . . 8 . 3 CYS H H 9.080 . . 9 . 3 CYS HA H 5.005 . . 10 . 3 CYS HB2 H 2.542 . . 11 . 3 CYS HB3 H 4.602 . . 12 . 4 CYS H H 9.041 . . 13 . 4 CYS HA H 5.432 . . 14 . 4 CYS HB2 H 2.897 . . 15 . 5 PRO HB2 H 2.023 . . 16 . 5 PRO HB3 H 1.930 . . 17 . 5 PRO HG2 H 2.887 . . 18 . 5 PRO HD2 H 3.997 . . 19 . 5 PRO HD3 H 3.794 . . 20 . 6 SER H H 7.000 . . 21 . 6 SER HA H 4.779 . . 22 . 6 SER HB2 H 4.032 . . 23 . 7 ILE H H 9.226 . . 24 . 7 ILE HA H 4.122 . . 25 . 7 ILE HB H 1.982 . . 26 . 7 ILE HG2 H 1.041 . . 27 . 7 ILE HG12 H 1.724 . . 28 . 7 ILE HG13 H 1.340 . . 29 . 7 ILE HD1 H 0.972 . . 30 . 8 VAL H H 7.680 . . 31 . 8 VAL HA H 3.769 . . 32 . 8 VAL HB H 2.039 . . 33 . 8 VAL HG1 H 1.076 . . 34 . 8 VAL HG2 H 0.987 . . 35 . 9 ALA H H 8.083 . . 36 . 9 ALA HA H 4.493 . . 37 . 9 ALA HB H 1.700 . . 38 . 10 ARG H H 7.794 . . 39 . 10 ARG HA H 4.609 . . 40 . 10 ARG HB2 H 2.034 . . 41 . 10 ARG HB3 H 1.714 . . 42 . 10 ARG HD2 H 3.430 . . 43 . 10 ARG HE H 9.690 . . 44 . 10 ARG HH11 H 6.640 . . 45 . 10 ARG HH12 H 6.640 . . 46 . 10 ARG HH21 H 7.061 . . 47 . 10 ARG HH22 H 7.061 . . 48 . 11 SER H H 8.411 . . 49 . 11 SER HA H 4.064 . . 50 . 11 SER HB2 H 4.093 . . 51 . 12 ASN H H 8.569 . . 52 . 12 ASN HA H 4.540 . . 53 . 12 ASN HB2 H 3.181 . . 54 . 12 ASN HB3 H 2.710 . . 55 . 12 ASN HD21 H 6.721 . . 56 . 12 ASN HD22 H 7.555 . . 57 . 13 PHE H H 9.305 . . 58 . 13 PHE HA H 3.960 . . 59 . 13 PHE HB2 H 3.831 . . 60 . 13 PHE HB3 H 3.557 . . 61 . 13 PHE HD1 H 7.220 . . 62 . 13 PHE HE1 H 7.461 . . 63 . 13 PHE HZ H 7.330 . . 64 . 14 ASN H H 8.748 . . 65 . 14 ASN HB2 H 2.774 . . 66 . 14 ASN HB3 H 3.314 . . 67 . 14 ASN HD21 H 7.064 . . 68 . 14 ASN HD22 H 7.817 . . 69 . 15 VAL H H 8.252 . . 70 . 15 VAL HA H 3.698 . . 71 . 15 VAL HB H 2.227 . . 72 . 15 VAL HG1 H 1.156 . . 73 . 15 VAL HG2 H 0.990 . . 74 . 16 CYS H H 9.302 . . 75 . 16 CYS HA H 3.823 . . 76 . 16 CYS HB2 H 2.600 . . 77 . 16 CYS HB3 H 2.465 . . 78 . 17 ARG H H 7.718 . . 79 . 17 ARG HA H 4.057 . . 80 . 17 ARG HB2 H 1.854 . . 81 . 17 ARG HB3 H 1.703 . . 82 . 17 ARG HG2 H 1.267 . . 83 . 17 ARG HG3 H 1.273 . . 84 . 17 ARG HD2 H 3.250 . . 85 . 17 ARG HD3 H 2.600 . . 86 . 17 ARG HE H 7.420 . . 87 . 18 LEU H H 7.639 . . 88 . 18 LEU HA H 4.211 . . 89 . 18 LEU HB2 H 2.078 . . 90 . 18 LEU HB3 H 1.635 . . 91 . 18 LEU HD1 H 1.010 . . 92 . 18 LEU HD2 H 0.930 . . 93 . 19 PRO HD2 H 4.070 . . 94 . 19 PRO HD3 H 3.963 . . 95 . 20 GLY H H 8.200 . . 96 . 20 GLY HA2 H 3.486 . . 97 . 20 GLY HA3 H 3.170 . . 98 . 21 THR H H 6.930 . . 99 . 21 THR HA H 4.030 . . 100 . 21 THR HB H 3.860 . . 101 . 21 THR HG2 H 1.338 . . 102 . 22 SER H H 8.202 . . 103 . 22 SER HA H 4.064 . . 104 . 22 SER HB2 H 3.539 . . 105 . 23 GLU H H 9.685 . . 106 . 23 GLU HA H 3.422 . . 107 . 23 GLU HB2 H 2.021 . . 108 . 23 GLU HB3 H 1.767 . . 109 . 23 GLU HG2 H 2.887 . . 110 . 23 GLU HG3 H 2.882 . . 111 . 24 ALA H H 8.597 . . 112 . 24 ALA HA H 4.104 . . 113 . 24 ALA HB H 1.470 . . 114 . 25 ILE H H 7.442 . . 115 . 25 ILE HA H 3.794 . . 116 . 25 ILE HB H 2.050 . . 117 . 25 ILE HG2 H 0.817 . . 118 . 25 ILE HG12 H 1.180 . . 119 . 25 ILE HG13 H 1.100 . . 120 . 26 CYS H H 8.327 . . 121 . 26 CYS HA H 4.674 . . 122 . 26 CYS HB2 H 2.766 . . 123 . 26 CYS HB3 H 2.492 . . 124 . 27 ALA H H 9.431 . . 125 . 27 ALA HA H 4.105 . . 126 . 27 ALA HB H 1.556 . . 127 . 28 THR H H 7.676 . . 128 . 28 THR HA H 3.989 . . 129 . 28 THR HG2 H 1.130 . . 130 . 29 TYR H H 7.921 . . 131 . 29 TYR HA H 4.435 . . 132 . 29 TYR HB2 H 3.238 . . 133 . 29 TYR HB3 H 3.050 . . 134 . 29 TYR HD1 H 7.252 . . 135 . 29 TYR HE1 H 6.764 . . 136 . 30 THR H H 7.592 . . 137 . 30 THR HA H 4.645 . . 138 . 30 THR HB H 4.744 . . 139 . 30 THR HG2 H 1.434 . . 140 . 31 GLY H H 8.038 . . 141 . 31 GLY HA2 H 3.960 . . 142 . 31 GLY HA3 H 3.563 . . 143 . 32 CYS H H 7.759 . . 144 . 32 CYS HA H 5.192 . . 145 . 32 CYS HB2 H 2.871 . . 146 . 32 CYS HB3 H 2.497 . . 147 . 33 ILE H H 9.047 . . 148 . 33 ILE HA H 4.770 . . 149 . 33 ILE HB H 1.616 . . 150 . 33 ILE HG2 H 0.606 . . 151 . 33 ILE HG12 H 1.095 . . 152 . 33 ILE HG13 H 0.817 . . 153 . 33 ILE HD1 H 0.160 . . 154 . 34 ILE H H 8.160 . . 155 . 34 ILE HA H 4.738 . . 156 . 34 ILE HB H 1.636 . . 157 . 34 ILE HG2 H 0.775 . . 158 . 34 ILE HG12 H 1.373 . . 159 . 34 ILE HG13 H 1.100 . . 160 . 35 ILE H H 8.490 . . 161 . 35 ILE HA H 4.998 . . 162 . 35 ILE HB H 2.040 . . 163 . 35 ILE HG2 H 0.816 . . 164 . 35 ILE HG12 H 1.467 . . 165 . 35 ILE HG13 H 0.965 . . 166 . 35 ILE HD1 H 0.773 . . 167 . 36 PRO HA H 4.603 . . 168 . 36 PRO HD2 H 3.795 . . 169 . 37 GLY H H 7.963 . . 170 . 37 GLY HA2 H 4.080 . . 171 . 38 ALA H H 8.472 . . 172 . 38 ALA HB H 1.446 . . 173 . 39 THR H H 7.716 . . 174 . 39 THR HA H 4.552 . . 175 . 39 THR HB H 3.959 . . 176 . 39 THR HG2 H 1.192 . . 177 . 40 CYS H H 8.762 . . 178 . 40 CYS HA H 4.880 . . 179 . 40 CYS HB2 H 2.634 . . 180 . 40 CYS HB3 H 3.446 . . 181 . 41 PRO HA H 4.612 . . 182 . 41 PRO HB2 H 2.420 . . 183 . 41 PRO HB3 H 2.226 . . 184 . 41 PRO HD2 H 3.813 . . 185 . 41 PRO HD3 H 3.676 . . 186 . 42 GLY H H 8.837 . . 187 . 42 GLY HA2 H 3.852 . . 188 . 43 ASP H H 8.389 . . 189 . 43 ASP HA H 4.683 . . 190 . 43 ASP HB2 H 3.039 . . 191 . 43 ASP HB3 H 2.846 . . 192 . 44 TYR H H 8.105 . . 193 . 44 TYR HA H 4.475 . . 194 . 44 TYR HB2 H 2.408 . . 195 . 44 TYR HB3 H 2.951 . . 196 . 44 TYR HD1 H 6.835 . . 197 . 44 TYR HE1 H 6.918 . . 198 . 45 ALA H H 7.668 . . 199 . 45 ALA HA H 4.486 . . 200 . 45 ALA HB H 1.370 . . 201 . 46 ASN H H 8.078 . . 202 . 46 ASN HA H 4.679 . . 203 . 46 ASN HB2 H 2.550 . . 204 . 46 ASN HB3 H 1.913 . . 205 . 46 ASN HD21 H 6.701 . . 206 . 46 ASN HD22 H 6.987 . . stop_ save_