data_21022 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; MDCSGCSRPG cyclic + copper(I) from acidic ; _BMRB_accession_number 21022 _BMRB_flat_file_name bmr21022.str _Entry_type new _Submission_date 2012-08-02 _Accession_date 2012-08-02 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details ; MDCSGCSRPG head-to-tail cyclic peptide, derived from copper(I) metallochaperone protein binding sites, with Cu(I) from acidic conditions, without using any constraints to the metal atom, lower energy ensemble (A). ; loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Shoshan Michal S . 2 Shalev Deborah E . 3 Tshuva Edit Y . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 structure_coordinate_set 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 48 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-03-21 original author 'original release; coordinate file annotated by PDBj' stop_ loop_ _Related_BMRB_accession_number _Relationship 21023 'MDCSGCSRPG head-to-tail cyclic peptide + Cu(I) no metal constraint - high energy ensemble (B)' 21024 'MDCSGCSRPG cyclic peptide bound to Cu(I) from acidic conditions' 21025 'MDCSGCSRPG+Zn from acidic conditions' 21026 'MDCSGCSRPG + Zn from basic conditions' 21027 'MDCSGCSRPG + Zn from basic conditions - tridentate binding' 21028 'MDCSGCSRPG-Zn-water complex from acidic conditions' stop_ save_ ############################# # Citation for this entry # ############################# save_Our_article _Saveframe_category entry_citation _Citation_full . _Citation_title 'Peptide Models of Cu(I) and Zn(II) Metallochaperones: The Effect of pH on Coordination and Mechanistic Implications.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 23458158 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Shoshan Michal S. . 2 Shalev Deborah E. . 3 Tshuva Edit Y. . stop_ _Journal_abbreviation 'Inorg. Chem.' _Journal_name_full 'Inorganic chemistry' _Journal_volume 52 _Journal_issue 6 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 2993 _Page_last 3000 _Year 2013 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name MDCSGCSRPG _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label MDCSGCSRPG $MDCSGCSRPG 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_MDCSGCSRPG _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common MDCSGCSRPG _Molecular_mass 1013.144 _Mol_thiol_state 'all free' _Details 'Head-to-tail cyclic peptide' ############################## # Polymer residue sequence # ############################## _Residue_count 10 _Mol_residue_sequence MDCSGCSRPG loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 MET 2 2 ASP 3 3 CYS 4 4 SER 5 5 GLY 6 6 CYS 7 7 SER 8 8 ARG 9 9 PRO 10 10 GLY stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ######################################## # Molecular bond linkage definitions # ######################################## save_crosslink_bonds _Saveframe_category crosslink_bonds loop_ _Bond_order _Bond_type _Atom_one_mol_system_component_name _Atom_one_residue_seq_code _Atom_one_residue_label _Atom_one_atom_name _Atom_two_mol_system_component_name _Atom_two_residue_seq_code _Atom_two_residue_label _Atom_two_atom_name single peptide MDCSGCSRPG 1 MET N MDCSGCSRPG 10 GLY C stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $MDCSGCSRPG . . . . . . 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 $MDCSGCSRPG 'recombinant technology' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details ; The peptide was dissolved in triple-distilled water (TDW) at pH 3.0. After lyophilization the apo peptide (2.0 mg, 2.01 umol) was dissolved in DMSO-d6 (500 uL) and was used as a control solution. In a separate flask, the peptide (2.0 mg, 2.01 umol) was dissolved in DMSO-d6 (450 uL) and CuCl was added from a stock solution (50 uL, 40.0 mM) in DMSO-d6, giving a dilution factor of 10 and a final CuCl concentration of 4.0 mM. All work was performed in a nitrogen glove-box. Samples remained colorless throughout the measurement. ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $MDCSGCSRPG 4.0 mM 'natural abundance' DMSO solvent mM [U-2H] CuCl 4.0 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version 1.3 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . 'Koradi, Billeter and Wuthrich' . . Goddard . . 'Schwieters, Kuszewski, Tjandra and Clore' . . 'Chimera UCSF' 'Pettersen, E. F.; Goddard, T. D.; Huang, C. C.; Couch, G. S.; Greenblatt, D. M.; Meng, E. C.; Ferrin, T. E. Journal of Computational Chemistry 2004, 25, 1605.' . stop_ loop_ _Task collection processing 'chemical shift assignment' 'peak picking' 'structure solution' refinement 'data analysis' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'AVANCE DMX' _Field_strength 600 _Details '+ XYZ gradients, selective probe' save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _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_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details '5 mm NMR tube' loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 298 0.1 K pH* 3.0 0.3 pH stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_DMSO _Saveframe_category chemical_shift_reference _Details 'Relative to DMSO at 2.50 ppm' 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 DMSO H 1 'methyl protons' ppm 2.50 internal direct . . . 1 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_MDC+Cu-acidic _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $TOPSPIN stop_ loop_ _Experiment_label '2D 1H-1H COSY' '2D 1H-1H TOCSY' '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_DMSO _Mol_system_component_name MDCSGCSRPG _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 MET H H 6.99 . . 2 1 1 MET HA H 4.49 . . 3 1 1 MET HB2 H 2.36 . . 4 1 1 MET HB3 H 1.89 . . 5 1 1 MET HG2 H 2.58 . . 6 1 1 MET HG3 H 2.58 . . 7 2 2 ASP H H 8.80 . . 8 2 2 ASP HA H 4.62 . . 9 2 2 ASP HB2 H 2.77 . . 10 2 2 ASP HB3 H 2.46 . . 11 3 3 CYS H H 7.63 . . 12 3 3 CYS HA H 4.77 . . 13 3 3 CYS HB2 H 2.97 . . 14 3 3 CYS HB3 H 2.84 . . 15 4 4 SER H H 9.09 . . 16 4 4 SER HA H 4.14 . . 17 4 4 SER HB2 H 3.69 . . 18 4 4 SER HB3 H 3.69 . . 19 5 5 GLY H H 8.37 . . 20 5 5 GLY HA2 H 3.91 . . 21 5 5 GLY HA3 H 3.49 . . 22 6 6 CYS H H 7.27 . . 23 6 6 CYS HA H 4.82 . . 24 6 6 CYS HB2 H 3.28 . . 25 6 6 CYS HB3 H 2.83 . . 26 7 7 SER H H 8.26 . . 27 7 7 SER HA H 4.37 . . 28 7 7 SER HB2 H 3.72 . . 29 7 7 SER HB3 H 3.72 . . 30 8 8 ARG H H 7.69 . . 31 8 8 ARG HA H 4.59 . . 32 8 8 ARG HB2 H 1.79 . . 33 8 8 ARG HB3 H 1.69 . . 34 8 8 ARG HD2 H 3.11 . . 35 8 8 ARG HD3 H 3.11 . . 36 8 8 ARG HE H 7.38 . . 37 8 8 ARG HG2 H 1.56 . . 38 8 8 ARG HG3 H 1.56 . . 39 9 9 PRO HA H 4.20 . . 40 9 9 PRO HB2 H 2.12 . . 41 9 9 PRO HB3 H 1.74 . . 42 9 9 PRO HD2 H 3.56 . . 43 9 9 PRO HD3 H 3.56 . . 44 9 9 PRO HG2 H 1.98 . . 45 9 9 PRO HG3 H 1.87 . . 46 10 10 GLY H H 8.80 . . 47 10 10 GLY HA2 H 3.90 . . 48 10 10 GLY HA3 H 3.38 . . stop_ save_