data_18750 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Chemical shift of E coli. IscU Prolyl residues in S-states ; _BMRB_accession_number 18750 _BMRB_flat_file_name bmr18750.str _Entry_type original _Submission_date 2012-10-01 _Accession_date 2012-10-01 _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 Dai Ziqi . . 2 Tonelli Marco . . 3 Markley John . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 3 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 25 "13C chemical shifts" 16 "15N chemical shifts" 2 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-02-12 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 18754 'IscU Prolyl residues in D-states' stop_ _Original_release_date 2013-02-12 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Metamorphic Protein IscU Changes Conformation by cis-trans Isomerizations of Two Peptidyl-Prolyl Peptide Bonds.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 23110687 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Dai Ziqi . . 2 Tonelli Marco . . 3 Markley John L. . stop_ _Journal_abbreviation Biochemistry _Journal_name_full Biochemistry _Journal_volume 51 _Journal_issue 48 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 9595 _Page_last 9602 _Year 2012 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name IscU _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label S-state $IscU 'Zinc ion' $entity_ZN 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_IscU _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common IscU _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 128 _Mol_residue_sequence ; MAYSEKVIDHYENPRNVGSF DNNDENVGSGMVGAPACGDV MKLQIKVNDEGIIEDARFKT YGCGSAIASSSLVTEWVKGK SLDEAQAIKNTDIAEELELP PVKIHCSILAEDAIKAAIAD YKSKREAK ; loop_ _Residue_seq_code _Residue_label 1 MET 2 ALA 3 TYR 4 SER 5 GLU 6 LYS 7 VAL 8 ILE 9 ASP 10 HIS 11 TYR 12 GLU 13 ASN 14 PRO 15 ARG 16 ASN 17 VAL 18 GLY 19 SER 20 PHE 21 ASP 22 ASN 23 ASN 24 ASP 25 GLU 26 ASN 27 VAL 28 GLY 29 SER 30 GLY 31 MET 32 VAL 33 GLY 34 ALA 35 PRO 36 ALA 37 CYS 38 GLY 39 ASP 40 VAL 41 MET 42 LYS 43 LEU 44 GLN 45 ILE 46 LYS 47 VAL 48 ASN 49 ASP 50 GLU 51 GLY 52 ILE 53 ILE 54 GLU 55 ASP 56 ALA 57 ARG 58 PHE 59 LYS 60 THR 61 TYR 62 GLY 63 CYS 64 GLY 65 SER 66 ALA 67 ILE 68 ALA 69 SER 70 SER 71 SER 72 LEU 73 VAL 74 THR 75 GLU 76 TRP 77 VAL 78 LYS 79 GLY 80 LYS 81 SER 82 LEU 83 ASP 84 GLU 85 ALA 86 GLN 87 ALA 88 ILE 89 LYS 90 ASN 91 THR 92 ASP 93 ILE 94 ALA 95 GLU 96 GLU 97 LEU 98 GLU 99 LEU 100 PRO 101 PRO 102 VAL 103 LYS 104 ILE 105 HIS 106 CYS 107 SER 108 ILE 109 LEU 110 ALA 111 GLU 112 ASP 113 ALA 114 ILE 115 LYS 116 ALA 117 ALA 118 ILE 119 ALA 120 ASP 121 TYR 122 LYS 123 SER 124 LYS 125 ARG 126 GLU 127 ALA 128 LYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-08-12 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 15967 IscU(D39A) 100.00 128 99.22 99.22 6.61e-86 BMRB 16245 IscU 100.00 130 100.00 100.00 4.86e-87 BMRB 16603 IscU 100.00 128 99.22 99.22 6.61e-86 BMRB 17282 IscU 100.00 128 100.00 100.00 5.02e-87 BMRB 17836 IscU 100.00 128 100.00 100.00 5.02e-87 BMRB 17837 IscU 100.00 128 100.00 100.00 5.02e-87 BMRB 17844 IscU 100.00 128 100.00 100.00 5.02e-87 BMRB 18359 IscU(D39V) 100.00 128 99.22 99.22 1.03e-85 BMRB 18360 IscU(E111A) 100.00 128 99.22 99.22 3.70e-86 BMRB 18361 IscU(N90A) 100.00 128 99.22 99.22 5.55e-86 BMRB 18362 IscU(S107A) 100.00 128 99.22 100.00 1.74e-86 BMRB 18381 IscU 100.00 128 100.00 100.00 5.02e-87 BMRB 18754 IscU 100.00 128 100.00 100.00 5.02e-87 PDB 2KQK "Solution Structure Of Apo-Iscu(D39a)" 100.00 128 99.22 99.22 6.61e-86 PDB 2L4X "Solution Structure Of Apo-Iscu(Wt)" 100.00 128 100.00 100.00 5.02e-87 PDB 3LVL "Crystal Structure Of E.Coli Iscs-Iscu Complex" 99.22 129 100.00 100.00 5.61e-86 DBJ BAA16423 "scaffold protein [Escherichia coli str. K12 substr. W3110]" 100.00 128 100.00 100.00 5.02e-87 DBJ BAB36818 "NifU-like protein [Escherichia coli O157:H7 str. Sakai]" 100.00 128 100.00 100.00 5.02e-87 DBJ BAG78339 "conserved hypothetical protein [Escherichia coli SE11]" 100.00 128 100.00 100.00 5.02e-87 DBJ BAH64655 "hypothetical protein KP1_4113 [Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044]" 100.00 128 97.66 100.00 5.68e-85 DBJ BAI26774 "scaffold protein IscU [Escherichia coli O26:H11 str. 11368]" 100.00 128 100.00 100.00 5.02e-87 EMBL CAD02745 "NifU-like protein [Salmonella enterica subsp. enterica serovar Typhi str. CT18]" 100.00 128 98.44 100.00 9.37e-86 EMBL CAP76981 "NifU-like protein [Escherichia coli LF82]" 100.00 128 99.22 99.22 3.04e-86 EMBL CAQ32902 "scaffold protein involved in iron-sulfur cluster assembly [Escherichia coli BL21(DE3)]" 100.00 128 100.00 100.00 5.02e-87 EMBL CAQ88187 "scaffold protein [Escherichia fergusonii ATCC 35469]" 100.00 128 100.00 100.00 5.02e-87 EMBL CAQ99420 "scaffold protein [Escherichia coli IAI1]" 100.00 128 100.00 100.00 5.02e-87 GB AAC75582 "iron-sulfur cluster assembly scaffold protein [Escherichia coli str. K-12 substr. MG1655]" 100.00 128 100.00 100.00 5.02e-87 GB AAG57643 "orf, hypothetical protein [Escherichia coli O157:H7 str. EDL933]" 100.00 128 100.00 100.00 5.02e-87 GB AAL21436 "NifU homolog [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]" 100.00 128 98.44 100.00 9.37e-86 GB AAN44075 "conserved hypothetical protein [Shigella flexneri 2a str. 301]" 100.00 128 100.00 100.00 5.02e-87 GB AAN81505 "NifU-like protein [Escherichia coli CFT073]" 100.00 128 100.00 100.00 5.02e-87 PIR AE0824 "NifU-like protein [imported] - Salmonella enterica subsp. enterica serovar Typhi (strain CT18)" 100.00 128 98.44 100.00 9.37e-86 REF NP_311422 "scaffold protein [Escherichia coli O157:H7 str. Sakai]" 100.00 128 100.00 100.00 5.02e-87 REF NP_417024 "iron-sulfur cluster assembly scaffold protein [Escherichia coli str. K-12 substr. MG1655]" 100.00 128 100.00 100.00 5.02e-87 REF NP_457073 "NifU-like protein [Salmonella enterica subsp. enterica serovar Typhi str. CT18]" 100.00 128 98.44 100.00 9.37e-86 REF NP_461477 "iron-sulfur cluster assembly scaffold protein [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]" 100.00 128 98.44 100.00 9.37e-86 REF NP_708368 "scaffold protein [Shigella flexneri 2a str. 301]" 100.00 128 100.00 100.00 5.02e-87 SP P0ACD4 "RecName: Full=Iron-sulfur cluster assembly scaffold protein IscU; AltName: Full=Sulfur acceptor protein IscU" 100.00 128 100.00 100.00 5.02e-87 SP P0ACD5 "RecName: Full=Iron-sulfur cluster assembly scaffold protein IscU; AltName: Full=Sulfur acceptor protein IscU" 100.00 128 100.00 100.00 5.02e-87 SP P0ACD6 "RecName: Full=Iron-sulfur cluster assembly scaffold protein IscU; AltName: Full=Sulfur acceptor protein IscU" 100.00 128 100.00 100.00 5.02e-87 SP P0ACD7 "RecName: Full=Iron-sulfur cluster assembly scaffold protein IscU; AltName: Full=Sulfur acceptor protein IscU" 100.00 128 100.00 100.00 5.02e-87 stop_ save_ ############# # Ligands # ############# save_ZN _Saveframe_category ligand _Mol_type "non-polymer (NON-POLYMER)" _Name_common 'ZINC ION' _BMRB_code ZN _PDB_code ZN _Molecular_mass 65.409 _Mol_charge 2 _Mol_paramagnetic . _Mol_aromatic no _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons ZN ZN ZN . 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 _Strain _Gene_mnemonic $IscU 'E. coli' 562 Bacteria . Escherichia coli BL21 iscU 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 $IscU 'recombinant technology' . Escherichia coli . pTrc99A stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_13C-15N-Pro _Saveframe_category sample _Sample_type solution _Details 'mM EDTA, 5 mM DTT, 150 mM NaCl, 50 MDSS, and 50 M NaN3 in 10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $IscU . mM 1 5 '[U-13C; U-15N]-Pro' $entity_ZN . mM 1 5 'natural abundance' D2O 10 % . . 'natural abundance' DSS 50 uM . . 'natural abundance' EDTA 0.5 mM . . 'natural abundance' DTT 5 mM . . 'natural abundance' 'sodium azide' 50 uM . . 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_jaulan _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _Details . save_ save_fleckvieh _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 900 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-13C_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $13C-15N-Pro save_ save_3D_HCCH-TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HCCH-TOCSY' _Sample_label $13C-15N-Pro save_ save_3D_1H-13C_NOESY_aliphatic_3 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-13C NOESY aliphatic' _Sample_label $13C-15N-Pro save_ ####################### # Sample conditions # ####################### save_with_Zn _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 1 . mM pH 8 . pH pressure 1 . atm temperature 298 . 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 C 13 'methyl protons' ppm 0 external indirect . . . 0.10132918 DSS H 1 'methyl protons' ppm 0 external direct . . . 1 DSS N 15 'methyl protons' ppm 0 external indirect . . . 0.251449530 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-13C HSQC' '3D HCCH-TOCSY' '3D 1H-13C NOESY aliphatic' stop_ loop_ _Sample_label $13C-15N-Pro stop_ _Sample_conditions_label $with_Zn _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name S-state _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 14 14 PRO HA H 4.226 0.0114 1 2 14 14 PRO HB2 H 2.288 0.0125 . 3 14 14 PRO HB3 H 1.919 0.0075 . 4 14 14 PRO HG2 H 2.069 0.0005 . 5 14 14 PRO HG3 H 2.017 0.0255 . 6 14 14 PRO HD2 H 3.858 0 . 7 14 14 PRO HD3 H 3.620 0 . 8 14 14 PRO CA C 64.79 0.0482 1 9 14 14 PRO CB C 31.98 0.0492 1 10 14 14 PRO CG C 27.35 0.0508 1 11 14 14 PRO CD C 50.65 0 1 12 35 35 PRO HA H 4.410 0.0138 1 13 35 35 PRO HG2 H 2.086 0.089 . 14 35 35 PRO HD2 H 3.651 0.0667 . 15 35 35 PRO HD3 H 3.730 0.078 . 16 35 35 PRO CA C 63.06 0.1048 1 17 35 35 PRO CB C 32.05 0.0457 1 18 35 35 PRO CG C 27.40 0.0467 1 19 35 35 PRO CD C 50.49 0.0667 1 20 35 35 PRO N N 135.7 0.1595 1 21 100 100 PRO HA H 4.846 0.012 1 22 100 100 PRO HB2 H 2.406 0.008 . 23 100 100 PRO HB3 H 2.037 0.012 . 24 100 100 PRO HG2 H 1.837 0.014 . 25 100 100 PRO HG3 H 2.169 0.008 . 26 100 100 PRO HD2 H 4.010 0.025 . 27 100 100 PRO HD3 H 3.707 0.076 . 28 100 100 PRO CA C 61.20 0.0907 1 29 100 100 PRO CB C 30.91 0.0737 1 30 100 100 PRO CG C 27.25 0.0995 1 31 100 100 PRO CD C 50.53 0.0822 1 32 101 101 PRO HA H 4.204 0.013 1 33 101 101 PRO HB2 H 2.380 0.039 . 34 101 101 PRO HB3 H 2.006 0.029 . 35 101 101 PRO HG2 H 2.222 0.041 . 36 101 101 PRO HG3 H 2.042 0.000 . 37 101 101 PRO HD2 H 3.300 0.009 . 38 101 101 PRO HD3 H 3.112 0.017 . 39 101 101 PRO CA C 66.13 0.13 1 40 101 101 PRO CB C 32.00 0.06 1 41 101 101 PRO CG C 27.45 0.08 1 42 101 101 PRO CD C 50.35 0.06 1 43 101 101 PRO N N 135.20 0.00 1 stop_ save_