data_6263 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution Structure of a Loop Truncated Mutant from D. gigas Rubredoxin, NMR ; _BMRB_accession_number 6263 _BMRB_flat_file_name bmr6263.str _Entry_type original _Submission_date 2004-07-16 _Accession_date 2004-07-16 _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 Pais T. M. . 2 Lamosa P. . . 3 'dos Santos' W. . . 4 LeGall J. . . 5 Turner D. L. . 6 Santos H. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 191 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2005-03-15 original author . stop_ _Original_release_date 2005-03-15 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structural Determinants of Protein Stabilization by Solutes: The Important of the Hair-pin Loop in Rubredoxins ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 15691333 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Pais T. M. . 2 Lamosa P. . . 3 'dos Santos' W. . . 4 LeGall J. . . 5 Turner D. L. . 6 Santos H. . . stop_ _Journal_abbreviation 'FEBS J.' _Journal_volume 272 _Journal_issue 4 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 999 _Page_last 1011 _Year 2005 _Details . loop_ _Keyword 'Truncated loop' stop_ save_ ################################## # Molecular system description # ################################## save_system _Saveframe_category molecular_system _Mol_system_name Rubredoxin _Abbreviation_common Rubredoxin _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label Rubredoxin $Rubredoxin stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'all other bound' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_Rubredoxin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common Rubredoxin _Abbreviation_common Rubredoxin _Molecular_mass . _Mol_thiol_state 'all other bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 39 _Mol_residue_sequence ; MDIYVCTVCGYEYDPAFEDL PDDWACPVCGASKDAFEKQ ; loop_ _Residue_seq_code _Residue_label 1 MET 2 ASP 3 ILE 4 TYR 5 VAL 6 CYS 7 THR 8 VAL 9 CYS 10 GLY 11 TYR 12 GLU 13 TYR 14 ASP 15 PRO 16 ALA 17 PHE 18 GLU 19 ASP 20 LEU 21 PRO 22 ASP 23 ASP 24 TRP 25 ALA 26 CYS 27 PRO 28 VAL 29 CYS 30 GLY 31 ALA 32 SER 33 LYS 34 ASP 35 ALA 36 PHE 37 GLU 38 LYS 39 GLN stop_ _Sequence_homology_query_date . _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 1SPW 'Solution Structure Of A Loop Truncated Mutant From D. Gigas Rubredoxin, Nmr' 100.00 39 100.00 100.00 1.47e-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 $Rubredoxin 'Desulfovibrio gigas' 879 Bacteria . Desulfovibrio gigas 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 $Rubredoxin 'recombinant technology' 'E. coli' Escherichia coli BL21DE pT7-7 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 $Rubredoxin 4 mM . H2O 90 % . D2O 10 % . NaCl 20 mM . stop_ save_ ############################ # Computer software used # ############################ save_XWINNMR _Saveframe_category software _Name xwinnmr _Version 3.1 loop_ _Task processing stop_ _Details 'Bruker and Rheinstetten' save_ save_DYANA _Saveframe_category software _Name DYANA _Version '1.4 with modifications' loop_ _Task 'iterative matrix relaxation' stop_ _Details 'Turner et al.' save_ save_XEASY _Saveframe_category software _Name XEASY _Version 1.3.10 loop_ _Task 'data analysis' stop_ _Details 'Wuthrich et al.' save_ save_GLOMSA _Saveframe_category software _Name GLOMSA _Version . loop_ _Task refinement stop_ _Details 'Guntert et al.' save_ save_PROCHECK-NMR _Saveframe_category software _Name ProcheckNMR _Version 3.4.4 loop_ _Task 'data analysis' stop_ _Details 'Laskowski et al.' save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label . save_ save_2D_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label . save_ save_COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name COSY _Sample_label . 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 '2D TOCSY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name COSY _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 'ionic strength' 20 . mM pH 7.6 . n/a pressure 1 . atm temperature 303 . K stop_ save_ save_sample_cond_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 20 . mM pH 7.6 . n/a pressure 1 . atm temperature 313 . 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 water H 1 . ppm 4.75 . . . . . 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 $chemical_shift_reference _Mol_system_component_name Rubredoxin _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 . 2 ASP HA H 4.548 0.001 1 2 . 2 ASP HB2 H 2.549 0.003 1 3 . 2 ASP HB3 H 2.432 0.009 1 4 . 3 ILE H H 8.000 0.002 1 5 . 3 ILE HA H 4.464 0.007 1 6 . 3 ILE HB H 1.689 0.003 1 7 . 3 ILE HG2 H 0.765 0.002 1 8 . 3 ILE HG12 H 1.334 0.005 2 9 . 3 ILE HG13 H 1.094 0.005 2 10 . 4 TYR H H 8.808 0.003 1 11 . 4 TYR HA H 5.120 0.006 1 12 . 4 TYR HB2 H 2.960 0.005 1 13 . 4 TYR HB3 H 2.898 0.005 1 14 . 4 TYR HD1 H 6.868 0.004 1 15 . 4 TYR HD2 H 6.868 0.004 1 16 . 4 TYR HE1 H 6.798 0.003 1 17 . 4 TYR HE2 H 6.798 0.003 1 18 . 5 VAL H H 9.078 0.005 1 19 . 5 VAL HA H 5.132 0.009 1 20 . 5 VAL HB H 1.842 0.005 1 21 . 5 VAL HG2 H 0.860 0.004 2 22 . 5 VAL HG1 H 0.795 0.003 2 23 . 6 CYS H H 9.274 0.003 1 24 . 6 CYS HA H 2.858 0.007 1 25 . 6 CYS HB3 H 3.089 0.007 1 26 . 6 CYS HB2 H 2.645 0.005 1 27 . 7 THR H H 8.438 0.002 1 28 . 7 THR HA H 4.078 0.005 1 29 . 7 THR HB H 4.363 0.002 1 30 . 7 THR HG2 H 1.372 0.002 1 31 . 7 THR HG1 H 5.920 0.008 1 32 . 8 VAL H H 9.056 0.003 1 33 . 8 VAL HA H 3.958 0.005 1 34 . 8 VAL HB H 2.608 0.002 1 35 . 8 VAL HG1 H 0.851 0.010 2 36 . 8 VAL HG2 H 0.814 0.001 2 37 . 9 CYS H H 9.048 0.003 1 38 . 9 CYS HA H 4.998 0.003 1 39 . 9 CYS HB2 H 3.296 0.003 1 40 . 9 CYS HB3 H 2.534 0.003 1 41 . 10 GLY H H 8.025 0.002 1 42 . 10 GLY HA2 H 3.699 0.001 1 43 . 10 GLY HA3 H 4.282 0.002 1 44 . 11 TYR H H 9.113 0.003 1 45 . 11 TYR HA H 4.250 0.006 1 46 . 11 TYR HB2 H 3.245 0.002 1 47 . 11 TYR HB3 H 3.080 0.005 1 48 . 11 TYR HD1 H 7.324 0.004 1 49 . 11 TYR HD2 H 7.324 0.004 1 50 . 11 TYR HE1 H 6.917 0.003 1 51 . 11 TYR HE2 H 6.917 0.003 1 52 . 12 GLU H H 7.323 0.004 1 53 . 12 GLU HA H 4.948 0.005 1 54 . 12 GLU HB2 H 1.797 0.009 1 55 . 12 GLU HB3 H 1.698 0.006 1 56 . 12 GLU HG2 H 2.417 0.003 1 57 . 12 GLU HG3 H 2.007 0.010 1 58 . 13 TYR H H 9.440 0.003 1 59 . 13 TYR HA H 4.718 0.006 1 60 . 13 TYR HB2 H 3.003 0.007 1 61 . 13 TYR HB3 H 2.950 0.011 1 62 . 13 TYR HE1 H 6.284 0.003 1 63 . 13 TYR HE2 H 6.284 0.003 1 64 . 13 TYR HD1 H 6.862 0.004 1 65 . 13 TYR HD2 H 6.862 0.004 1 66 . 14 ASP H H 7.906 0.004 1 67 . 14 ASP HA H 5.028 0.004 1 68 . 14 ASP HB3 H 2.681 0.008 1 69 . 14 ASP HB2 H 2.467 0.004 1 70 . 15 PRO HA H 4.176 0.005 1 71 . 15 PRO HB2 H 1.989 0.004 1 72 . 15 PRO HB3 H 1.880 0.011 1 73 . 15 PRO HG2 H 1.881 0.004 1 74 . 15 PRO HG3 H 1.665 0.010 1 75 . 15 PRO HD2 H 3.844 0.006 1 76 . 15 PRO HD3 H 3.660 0.010 1 77 . 16 ALA H H 8.211 0.003 1 78 . 16 ALA HA H 3.980 0.007 1 79 . 16 ALA HB H 1.207 0.003 1 80 . 17 PHE H H 7.944 0.004 1 81 . 17 PHE HA H 4.364 0.004 1 82 . 17 PHE HB2 H 3.092 0.008 1 83 . 17 PHE HB3 H 3.007 0.008 1 84 . 17 PHE HE1 H 6.536 0.008 3 85 . 17 PHE HZ H 6.720 0.005 1 86 . 17 PHE HD1 H 7.045 0.040 3 87 . 18 GLU H H 7.968 0.004 1 88 . 18 GLU HA H 4.226 0.004 1 89 . 18 GLU HB2 H 2.029 0.005 1 90 . 18 GLU HB3 H 1.906 0.002 1 91 . 18 GLU HG2 H 2.234 0.004 1 92 . 20 LEU H H 7.905 0.003 1 93 . 20 LEU HA H 4.038 0.002 1 94 . 20 LEU HB2 H 1.008 0.002 1 95 . 20 LEU HB3 H 0.806 0.044 1 96 . 20 LEU HD1 H -0.224 0.003 2 97 . 20 LEU HD2 H -0.364 0.006 2 98 . 21 PRO HA H 4.467 0.003 1 99 . 21 PRO HB3 H 2.386 0.006 1 100 . 21 PRO HB2 H 2.096 0.006 1 101 . 21 PRO HG2 H 2.094 0.011 2 102 . 21 PRO HD2 H 3.750 0.004 1 103 . 21 PRO HD3 H 3.271 0.006 1 104 . 22 ASP H H 8.539 0.001 1 105 . 22 ASP HA H 4.299 0.000 1 106 . 22 ASP HB2 H 2.651 0.001 1 107 . 22 ASP HB3 H 2.589 0.001 1 108 . 23 ASP H H 8.220 0.003 1 109 . 23 ASP HA H 4.604 0.001 1 110 . 23 ASP HB2 H 2.787 0.005 1 111 . 23 ASP HB3 H 2.561 0.000 1 112 . 24 TRP H H 7.390 0.002 1 113 . 24 TRP HA H 4.271 0.007 1 114 . 24 TRP HB2 H 3.144 0.008 1 115 . 24 TRP HB3 H 2.779 0.006 1 116 . 24 TRP HE3 H 6.403 0.002 1 117 . 24 TRP HZ3 H 6.528 0.012 1 118 . 24 TRP HD1 H 7.071 0.042 1 119 . 24 TRP HH2 H 6.714 0.008 1 120 . 25 ALA H H 6.535 0.012 1 121 . 25 ALA HA H 4.419 0.003 1 122 . 25 ALA HB H 0.891 0.004 1 123 . 26 CYS H H 9.349 0.002 1 124 . 26 CYS HA H 4.071 0.007 1 125 . 26 CYS HB2 H 3.192 0.003 2 126 . 27 PRO HA H 4.097 0.012 1 127 . 27 PRO HB2 H 1.675 0.008 1 128 . 27 PRO HB3 H 2.129 0.002 1 129 . 27 PRO HG2 H 1.346 0.001 1 130 . 27 PRO HG3 H 1.759 0.001 1 131 . 27 PRO HD2 H 3.483 0.007 2 132 . 28 VAL H H 8.683 0.005 1 133 . 28 VAL HA H 3.862 0.007 1 134 . 28 VAL HB H 2.639 0.002 1 135 . 28 VAL HG1 H 0.865 0.003 2 136 . 28 VAL HG2 H 0.744 0.008 2 137 . 29 CYS H H 8.676 0.005 1 138 . 29 CYS HA H 4.886 0.003 1 139 . 29 CYS HB2 H 3.247 0.003 1 140 . 29 CYS HB3 H 2.527 0.003 1 141 . 30 GLY H H 7.863 0.003 1 142 . 30 GLY HA2 H 3.629 0.001 1 143 . 30 GLY HA3 H 4.131 0.002 1 144 . 31 ALA H H 9.073 0.001 1 145 . 31 ALA HA H 4.192 0.004 1 146 . 31 ALA HB H 1.523 0.007 1 147 . 32 SER H H 8.240 0.002 1 148 . 32 SER HA H 4.570 0.002 1 149 . 32 SER HB2 H 4.335 0.004 1 150 . 32 SER HB3 H 4.073 0.006 1 151 . 33 LYS H H 8.423 0.002 1 152 . 33 LYS HA H 3.955 0.007 1 153 . 33 LYS HB3 H 1.761 0.005 1 154 . 33 LYS HB2 H 1.237 0.006 1 155 . 33 LYS HG2 H 1.523 0.006 1 156 . 33 LYS HG3 H 1.358 0.009 1 157 . 33 LYS HD2 H 1.468 0.001 2 158 . 34 ASP H H 8.283 0.006 1 159 . 34 ASP HA H 4.561 0.004 1 160 . 34 ASP HB2 H 2.764 0.003 1 161 . 34 ASP HB3 H 2.637 0.002 1 162 . 35 ALA H H 8.265 0.007 1 163 . 35 ALA HA H 4.470 0.003 1 164 . 35 ALA HB H 1.603 0.004 1 165 . 36 PHE H H 8.151 0.004 1 166 . 36 PHE HA H 5.230 0.004 1 167 . 36 PHE HB2 H 3.551 0.006 1 168 . 36 PHE HB3 H 2.738 0.011 1 169 . 36 PHE HZ H 7.793 0.003 1 170 . 36 PHE HD1 H 7.415 0.003 1 171 . 36 PHE HD2 H 7.415 0.003 1 172 . 36 PHE HE1 H 7.536 0.003 1 173 . 36 PHE HE2 H 7.536 0.003 1 174 . 37 GLU H H 8.966 0.004 1 175 . 37 GLU HA H 4.834 0.006 1 176 . 37 GLU HB3 H 1.984 0.005 1 177 . 37 GLU HB2 H 1.841 0.002 1 178 . 37 GLU HG2 H 2.214 0.002 2 179 . 38 LYS H H 8.736 0.003 1 180 . 38 LYS HA H 4.207 0.007 1 181 . 38 LYS HB2 H 1.604 0.004 1 182 . 38 LYS HB3 H 1.414 0.069 1 183 . 38 LYS HG2 H 1.104 0.007 1 184 . 38 LYS HG3 H 0.892 0.005 1 185 . 38 LYS HD2 H 1.502 0.004 2 186 . 38 LYS HE2 H 2.826 0.004 2 187 . 39 GLN H H 8.612 0.003 1 188 . 39 GLN HA H 4.103 0.004 1 189 . 39 GLN HB2 H 2.062 0.004 1 190 . 39 GLN HB3 H 1.753 0.003 1 191 . 39 GLN HG2 H 2.236 0.002 2 stop_ save_