data_17997 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of the Cd(II) form of Desulforedoxin ; _BMRB_accession_number 17997 _BMRB_flat_file_name bmr17997.str _Entry_type original _Submission_date 2011-10-12 _Accession_date 2011-10-12 _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 Goodfellow Brian J. . 2 Tavares Pedro . . 3 Romao Maria J. . 4 Czaja C. . . 5 Rusnak Frank . . 6 LeGall Jean . . 7 Moura Isabel . . 8 Moura Jose JG . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 194 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2011-11-02 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 17979 'Zn(II) form of Desulforedoxin' 5249 'Backbone chemical shifts for desulforedoxin' 5260 'Pseudocontact chemical shifts for [Fe(II)/Fe(II)]Dx' 5271 'Pseudocontact chemical shifts for [Fe(II)/Zn(II)]Dx' stop_ _Original_release_date 2011-11-02 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'The solution structure of desulforedoxin, a simple iron-sulfur protein - An NMR study of the zinc derivative' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Goodfellow Brian J. . 2 Tavares Pedro . . 3 Romao Maria . . 4 Czaja C. . . 5 Rusnak Frank . . 6 LeGall Jean . . 7 Moura Isabel . . 8 Moura Jose JG . stop_ _Journal_abbreviation 'J. Biol. Inorg. Chem.' _Journal_volume 1 _Journal_issue 4 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 341 _Page_last 354 _Year 1996 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Cd(II) form of Desulforedoxin' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label Desulforedoxin $Desulforedoxin 'Cd(II) ion' $CD 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_Desulforedoxin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity _Molecular_mass 3807.364 _Mol_thiol_state unknown _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 36 _Mol_residue_sequence ; ANEGDVYKCELCGQVVKVLE EGGGTLVCCGEDMVKQ ; loop_ _Residue_seq_code _Residue_label 1 ALA 2 ASN 3 GLU 4 GLY 5 ASP 6 VAL 7 TYR 8 LYS 9 CYS 10 GLU 11 LEU 12 CYS 13 GLY 14 GLN 15 VAL 16 VAL 17 LYS 18 VAL 19 LEU 20 GLU 21 GLU 22 GLY 23 GLY 24 GLY 25 THR 26 LEU 27 VAL 28 CYS 29 CYS 30 GLY 31 GLU 32 ASP 33 MET 34 VAL 35 LYS 36 GLN stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-10-14 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 17979 Desulforedoxin 100.00 36 100.00 100.00 1.41e-14 PDB 1CFW "Ga-Substituted Desulforedoxin" 100.00 36 100.00 100.00 1.41e-14 PDB 1DCD "Desulforedoxin Complexed With Cd2+" 100.00 36 100.00 100.00 1.41e-14 PDB 1DHG "Hg-Substituted Desulforedoxin" 100.00 36 100.00 100.00 1.41e-14 PDB 1DXG "Crystal Structure Of Desulforedoxin From Desulfovibrio Gigas At 1.8 A Resolution" 100.00 36 100.00 100.00 1.41e-14 PDB 2LK5 "Solution Structure Of The Zn(Ii) Form Of Desulforedoxin" 100.00 36 100.00 100.00 1.41e-14 PDB 2LK6 "Nmr Determination Of The Global Structure Of The Cd-113 Derivative Of Desulforedoxin" 100.00 36 100.00 100.00 1.41e-14 GB AAA23365 "desulforedoxin [Desulfovibrio gigas]" 100.00 37 100.00 100.00 1.33e-14 GB AGW15163 "Desulforedoxin [Desulfovibrio gigas DSM 1382 = ATCC 19364]" 100.00 37 100.00 100.00 1.33e-14 REF WP_021762290 "desulforedoxin [Desulfovibrio gigas]" 100.00 37 100.00 100.00 1.33e-14 SP P00273 "RecName: Full=Desulforedoxin; Short=DX" 100.00 37 100.00 100.00 1.33e-14 stop_ save_ ############# # Ligands # ############# save_CD _Saveframe_category ligand _Mol_type non-polymer _Name_common "CD (CADMIUM ION)" _BMRB_code . _PDB_code CD _Molecular_mass 112.411 _Mol_charge 2 _Mol_paramagnetic . _Mol_aromatic no _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Fri Oct 14 13:32:37 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons CD CD CD . 2 . ? stop_ _Mol_thiol_state . _Sequence_homology_query_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $Desulforedoxin '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 $Desulforedoxin 'recombinant technology' . Escherichia coli . DSRT77-2 stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details 'pH 7.0' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Desulforedoxin 2-4 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_DIANA _Saveframe_category software _Name DIANA _Version 2.8 loop_ _Vendor _Address _Electronic_address 'Guntert, Braun and Wuthrich' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_XEASY _Saveframe_category software _Name XEASY _Version 3.1 loop_ _Vendor _Address _Electronic_address 'Bartels et al.' . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model ARX _Field_strength 400 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _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_ save_NMR_spectrometer_expt _Saveframe_category NMR_applied_experiment _Experiment_name . _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 0 . M pH 7.0 . pH pressure 1 . atm temperature 303 . 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 H 1 'methyl protons' ppm 0.00 internal direct cylindrical 'separate tube (no insert) similar to the experimental sample tube' parallel 1.000000000 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' '2D DQF-COSY' '2D 1H-1H NOESY' 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 Desulforedoxin _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 ALA HA H 3.970 0.000 1 2 1 1 ALA HB H 1.502 0.005 1 3 2 2 ASN H H 8.353 0.001 1 4 2 2 ASN HA H 4.730 0.000 1 5 2 2 ASN HB2 H 2.621 0.004 2 6 2 2 ASN HB3 H 2.621 0.004 2 7 2 2 ASN HD21 H 6.762 0.000 2 8 2 2 ASN HD22 H 7.664 0.002 2 9 3 3 GLU H H 9.010 0.005 1 10 3 3 GLU HA H 3.325 0.001 1 11 3 3 GLU HB2 H 1.817 0.008 2 12 3 3 GLU HB3 H 1.817 0.008 2 13 3 3 GLU HG2 H 1.912 0.002 2 14 3 3 GLU HG3 H 2.186 0.006 2 15 4 4 GLY H H 8.927 0.004 1 16 4 4 GLY HA2 H 4.301 0.007 2 17 4 4 GLY HA3 H 3.342 0.008 2 18 5 5 ASP H H 7.941 0.004 1 19 5 5 ASP HA H 4.359 0.008 1 20 5 5 ASP HB2 H 2.916 0.004 2 21 5 5 ASP HB3 H 2.454 0.006 2 22 6 6 VAL H H 8.685 0.010 1 23 6 6 VAL HA H 4.815 0.009 1 24 6 6 VAL HB H 1.587 0.005 1 25 6 6 VAL HG1 H 0.587 0.010 2 26 6 6 VAL HG2 H 0.750 0.004 2 27 7 7 TYR H H 8.984 0.003 1 28 7 7 TYR HA H 4.790 0.001 1 29 7 7 TYR HB2 H 2.246 0.001 2 30 7 7 TYR HB3 H 2.609 0.001 2 31 7 7 TYR HD1 H 6.444 0.000 3 32 7 7 TYR HD2 H 6.445 0.003 3 33 7 7 TYR HE1 H 6.629 0.002 3 34 7 7 TYR HE2 H 6.634 0.001 3 35 8 8 LYS H H 8.818 0.002 1 36 8 8 LYS HA H 5.254 0.002 1 37 8 8 LYS HB2 H 1.643 0.003 2 38 8 8 LYS HB3 H 1.643 0.003 2 39 8 8 LYS HG2 H 0.924 0.008 2 40 8 8 LYS HG3 H 0.924 0.008 2 41 8 8 LYS HD2 H 1.200 0.008 2 42 8 8 LYS HD3 H 1.200 0.000 2 43 8 8 LYS HE2 H 2.592 0.012 2 44 8 8 LYS HE3 H 2.592 0.012 2 45 9 9 CYS H H 9.146 0.002 1 46 9 9 CYS HA H 4.655 0.000 1 47 9 9 CYS HB2 H 2.390 0.004 2 48 9 9 CYS HB3 H 3.140 0.005 2 49 10 10 GLU H H 9.366 0.007 1 50 10 10 GLU HA H 3.985 0.000 1 51 10 10 GLU HB2 H 1.730 0.005 2 52 10 10 GLU HB3 H 1.730 0.005 2 53 10 10 GLU HG2 H 1.971 0.000 2 54 10 10 GLU HG3 H 2.254 0.002 2 55 11 11 LEU H H 9.173 0.001 1 56 11 11 LEU HA H 4.242 0.002 1 57 11 11 LEU HB2 H 1.690 0.004 2 58 11 11 LEU HB3 H 1.690 0.004 2 59 11 11 LEU HG H 1.430 0.007 1 60 11 11 LEU HD1 H 0.756 0.015 2 61 11 11 LEU HD2 H 0.756 0.015 2 62 12 12 CYS H H 8.892 0.001 1 63 12 12 CYS HA H 4.872 0.000 1 64 12 12 CYS HB2 H 2.634 0.008 2 65 12 12 CYS HB3 H 3.148 0.007 2 66 13 13 GLY H H 7.567 0.003 1 67 13 13 GLY HA2 H 4.080 0.006 2 68 13 13 GLY HA3 H 3.511 0.000 2 69 14 14 GLN H H 8.446 0.005 1 70 14 14 GLN HA H 3.835 0.002 1 71 14 14 GLN HB2 H 1.813 0.008 2 72 14 14 GLN HB3 H 1.922 0.000 2 73 14 14 GLN HG2 H 2.235 0.003 2 74 14 14 GLN HG3 H 2.235 0.003 2 75 14 14 GLN HE21 H 5.908 0.001 2 76 14 14 GLN HE22 H 6.728 0.009 2 77 15 15 VAL H H 8.415 0.004 1 78 15 15 VAL HA H 4.999 0.004 1 79 15 15 VAL HB H 1.529 0.016 1 80 15 15 VAL HG1 H 0.764 0.012 2 81 15 15 VAL HG2 H 0.764 0.012 2 82 16 16 VAL H H 9.358 0.003 1 83 16 16 VAL HA H 5.372 0.003 1 84 16 16 VAL HB H 1.798 0.005 1 85 16 16 VAL HG2 H 0.567 0.015 2 86 17 17 LYS H H 9.044 0.008 1 87 17 17 LYS HA H 5.320 0.003 1 88 17 17 LYS HB2 H 1.499 0.010 2 89 17 17 LYS HB3 H 1.499 0.010 2 90 17 17 LYS HG2 H 1.080 0.011 2 91 17 17 LYS HG3 H 1.080 0.011 2 92 17 17 LYS HD2 H 0.633 0.017 2 93 17 17 LYS HD3 H 0.633 0.017 2 94 17 17 LYS HE2 H 2.779 0.008 2 95 17 17 LYS HE3 H 2.779 0.008 2 96 18 18 VAL H H 9.016 0.006 1 97 18 18 VAL HA H 3.910 0.003 1 98 18 18 VAL HB H 2.265 0.008 1 99 18 18 VAL HG1 H 0.522 0.005 2 100 18 18 VAL HG2 H 0.742 0.001 2 101 19 19 LEU H H 9.357 0.006 1 102 19 19 LEU HA H 4.348 0.001 1 103 19 19 LEU HB2 H 1.380 0.010 2 104 19 19 LEU HB3 H 1.380 0.010 2 105 19 19 LEU HG H 1.503 0.006 1 106 19 19 LEU HD1 H 0.742 0.000 2 107 19 19 LEU HD2 H 0.752 0.000 2 108 20 20 GLU H H 7.540 0.003 1 109 20 20 GLU HA H 4.536 0.000 1 110 20 20 GLU HB2 H 1.621 0.005 2 111 20 20 GLU HB3 H 1.621 0.005 2 112 20 20 GLU HG2 H 2.109 0.003 2 113 20 20 GLU HG3 H 1.937 0.003 2 114 21 21 GLU H H 8.710 0.004 1 115 21 21 GLU HA H 4.056 0.003 1 116 21 21 GLU HB2 H 2.221 0.007 2 117 21 21 GLU HB3 H 2.221 0.007 2 118 21 21 GLU HG2 H 1.844 0.013 2 119 21 21 GLU HG3 H 1.844 0.013 2 120 22 22 GLY H H 7.305 0.003 1 121 22 22 GLY HA2 H 3.958 0.000 2 122 22 22 GLY HA3 H 4.095 0.002 2 123 23 23 GLY H H 7.879 0.001 1 124 23 23 GLY HA2 H 3.518 0.000 2 125 23 23 GLY HA3 H 3.930 0.011 2 126 24 24 GLY H H 8.429 0.005 1 127 24 24 GLY HA2 H 3.820 0.013 2 128 24 24 GLY HA3 H 4.409 0.000 2 129 25 25 THR H H 8.758 0.006 1 130 25 25 THR HA H 4.007 0.004 1 131 25 25 THR HB H 3.782 0.004 1 132 25 25 THR HG2 H 0.921 0.003 1 133 26 26 LEU H H 8.014 0.010 1 134 26 26 LEU HA H 4.217 0.007 1 135 26 26 LEU HB2 H 1.140 0.007 2 136 26 26 LEU HB3 H 1.140 0.007 2 137 26 26 LEU HG H 0.924 0.004 1 138 26 26 LEU HD1 H -0.043 0.006 2 139 26 26 LEU HD2 H 0.503 0.005 2 140 27 27 VAL H H 9.224 0.004 1 141 27 27 VAL HA H 4.215 0.011 1 142 27 27 VAL HB H 1.387 0.006 1 143 27 27 VAL HG1 H 0.421 0.002 2 144 27 27 VAL HG2 H 0.650 0.008 2 145 28 28 CYS H H 8.314 0.003 1 146 28 28 CYS HA H 4.436 0.007 1 147 28 28 CYS HB2 H 2.417 0.013 2 148 28 28 CYS HB3 H 2.797 0.003 2 149 29 29 CYS H H 7.334 0.002 1 150 29 29 CYS HA H 3.824 0.008 1 151 29 29 CYS HB2 H 2.992 0.004 2 152 29 29 CYS HB3 H 2.894 0.004 2 153 30 30 GLY H H 8.120 0.004 1 154 30 30 GLY HA2 H 3.847 0.008 2 155 30 30 GLY HA3 H 3.223 0.005 2 156 31 31 GLU H H 7.787 0.002 1 157 31 31 GLU HA H 4.597 0.000 1 158 31 31 GLU HB2 H 2.154 0.003 2 159 31 31 GLU HB3 H 1.603 0.003 2 160 31 31 GLU HG2 H 1.910 0.000 2 161 31 31 GLU HG3 H 2.011 0.005 2 162 32 32 ASP H H 8.800 0.004 1 163 32 32 ASP HA H 4.428 0.004 1 164 32 32 ASP HB2 H 2.402 0.002 2 165 32 32 ASP HB3 H 2.402 0.002 2 166 33 33 MET H H 8.238 0.005 1 167 33 33 MET HA H 4.356 0.001 1 168 33 33 MET HB2 H 2.084 0.008 2 169 33 33 MET HB3 H 1.895 0.008 2 170 33 33 MET HG2 H 1.645 0.007 2 171 33 33 MET HG3 H 1.645 0.007 2 172 33 33 MET HE H 1.445 0.009 1 173 34 34 VAL H H 9.195 0.005 1 174 34 34 VAL HA H 4.046 0.002 1 175 34 34 VAL HB H 1.859 0.013 1 176 34 34 VAL HG1 H 0.950 0.008 2 177 34 34 VAL HG2 H 0.774 0.009 2 178 35 35 LYS H H 8.831 0.007 1 179 35 35 LYS HA H 3.193 0.002 1 180 35 35 LYS HB2 H 1.408 0.008 2 181 35 35 LYS HB3 H 1.408 0.008 2 182 35 35 LYS HG2 H 1.219 0.001 2 183 35 35 LYS HG3 H 1.219 0.001 2 184 35 35 LYS HD3 H 0.676 0.000 2 185 35 35 LYS HE2 H 2.755 0.001 2 186 35 35 LYS HE3 H 2.755 0.001 2 187 36 36 GLN H H 8.691 0.006 1 188 36 36 GLN HA H 3.871 0.006 1 189 36 36 GLN HB2 H 1.469 0.007 2 190 36 36 GLN HB3 H 1.469 0.007 2 191 36 36 GLN HG2 H 2.009 0.015 2 192 36 36 GLN HG3 H 1.904 0.003 2 193 36 36 GLN HE21 H 6.626 0.004 2 194 36 36 GLN HE22 H 7.410 0.007 2 stop_ save_