data_21028 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; MDCSGCSRPG-Zn-water complex from acidic conditions ; _BMRB_accession_number 21028 _BMRB_flat_file_name bmr21028.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-Zn-water complex from acidic conditions where Zn binds in a tetradentate manner' 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 2013-03-22 original author 'original release; coordinate file annotated by PDBj' stop_ loop_ _Related_BMRB_accession_number _Relationship 21022 'MDCSGCSRPG cyclic + copper(I) from acidic' 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' 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 + Zn acidic' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label MDCSGCSRPG $MDCSGCSRPG+Zn-H2O_acidic Zn(II) $entity_ZEM H2O $entity_HOH stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details 'MDCSGCSRPG head-to-tail cyclic peptide in complex with Zn(II) and water ligands from acidic conditions' save_ ######################## # Monomeric polymers # ######################## save_MDCSGCSRPG+Zn-H2O_acidic _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common MDCSGCSRPG+Zn-H2O_acidic _Molecular_mass . _Mol_thiol_state 'all other bound' _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_ ############# # Ligands # ############# save_ZEM _Saveframe_category ligand _Mol_type "non-polymer (NON-POLYMER)" _Name_common '20-OXO-PROTOPORPHYRIN IX CONTAINING ZN(II)' _BMRB_code ZEM _PDB_code ZEM _Molecular_mass 642.051 _Mol_charge 0 _Mol_paramagnetic . _Mol_aromatic yes _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C1A C1A C . 0 . ? C1B C1B C . 0 . ? C1C C1C C . 0 . ? C1D C1D C . 0 . ? C2A C2A C . 0 . ? C2B C2B C . 0 . ? C2C C2C C . 0 . ? C2D C2D C . 0 . ? C3A C3A C . 0 . ? C3B C3B C . 0 . ? C3C C3C C . 0 . ? C3D C3D C . 0 . ? C4A C4A C . 0 . ? C4B C4B C . 0 . ? C4C C4C C . 0 . ? C4D C4D C . 0 . ? CAA CAA C . 0 . ? CAB CAB C . 0 . ? CAC CAC C . 0 . ? CAD CAD C . 0 . ? CBA CBA C . 0 . ? CBB CBB C . 0 . ? CBC CBC C . 0 . ? CBD CBD C . 0 . ? CGA CGA C . 0 . ? CGD CGD C . 0 . ? CHA CHA C . 0 . ? CHB CHB C . 0 . ? CHC CHC C . 0 . ? CHD CHD C . 0 . ? CMA CMA C . 0 . ? CMB CMB C . 0 . ? CMC CMC C . 0 . ? CMD CMD C . 0 . ? H2A H2A H . 0 . ? H2D H2D H . 0 . ? HAA1 HAA1 H . 0 . ? HAA2 HAA2 H . 0 . ? HAB HAB H . 0 . ? HAC HAC H . 0 . ? HAD1 HAD1 H . 0 . ? HAD2 HAD2 H . 0 . ? HBA1 HBA1 H . 0 . ? HBA2 HBA2 H . 0 . ? HBB1 HBB1 H . 0 . ? HBB2 HBB2 H . 0 . ? HBC1 HBC1 H . 0 . ? HBC2 HBC2 H . 0 . ? HBD1 HBD1 H . 0 . ? HBD2 HBD2 H . 0 . ? HHA HHA H . 0 . ? HHC HHC H . 0 . ? HHD HHD H . 0 . ? HMA1 HMA1 H . 0 . ? HMA2 HMA2 H . 0 . ? HMA3 HMA3 H . 0 . ? HMB1 HMB1 H . 0 . ? HMB2 HMB2 H . 0 . ? HMB3 HMB3 H . 0 . ? HMC1 HMC1 H . 0 . ? HMC2 HMC2 H . 0 . ? HMC3 HMC3 H . 0 . ? HMD1 HMD1 H . 0 . ? HMD2 HMD2 H . 0 . ? HMD3 HMD3 H . 0 . ? HZ HZ H . 0 . ? NA NA N . 0 . ? NB NB N . 0 . ? NC NC N . 0 . ? ND ND N . 0 . ? O1A O1A O . 0 . ? O1D O1D O . 0 . ? O2A O2A O . 0 . ? O2D O2D O . 0 . ? OZ OZ O . 0 . ? ZN ZN ZN . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING ZN NA ? ? SING ZN NB ? ? SING ZN NC ? ? SING ZN ND ? ? SING NA C1A ? ? SING NA C4A ? ? SING NB C1B ? ? DOUB NB C4B ? ? SING NC C1C ? ? SING NC C4C ? ? SING ND C4D ? ? DOUB ND C1D ? ? SING C1A CHA ? ? DOUB C1A C2A ? ? DOUB CHA C4D ? ? SING CHA HHA ? ? SING C4D C3D ? ? DOUB C1B CHB ? ? SING C1B C2B ? ? SING CHB OZ ? ? SING CHB C4A ? ? SING OZ HZ ? ? DOUB C4A C3A ? ? DOUB C1C CHC ? ? SING C1C C2C ? ? SING CHC C4B ? ? SING CHC HHC ? ? SING C4B C3B ? ? SING C1D CHD ? ? SING C1D C2D ? ? DOUB CHD C4C ? ? SING CHD HHD ? ? SING C4C C3C ? ? SING C2A CAA ? ? SING C2A C3A ? ? SING CAA CBA ? ? SING CAA HAA1 ? ? SING CAA HAA2 ? ? SING C3A CMA ? ? SING CMA HMA1 ? ? SING CMA HMA2 ? ? SING CMA HMA3 ? ? SING CBA CGA ? ? SING CBA HBA1 ? ? SING CBA HBA2 ? ? DOUB CGA O1A ? ? SING CGA O2A ? ? SING O2A H2A ? ? SING C2B CMB ? ? DOUB C2B C3B ? ? SING CMB HMB1 ? ? SING CMB HMB2 ? ? SING CMB HMB3 ? ? SING C3B CAB ? ? DOUB CAB CBB ? ? SING CAB HAB ? ? SING CBB HBB1 ? ? SING CBB HBB2 ? ? SING C2C CMC ? ? DOUB C2C C3C ? ? SING CMC HMC1 ? ? SING CMC HMC2 ? ? SING CMC HMC3 ? ? SING C3C CAC ? ? DOUB CAC CBC ? ? SING CAC HAC ? ? SING CBC HBC1 ? ? SING CBC HBC2 ? ? SING C2D CMD ? ? DOUB C2D C3D ? ? SING CMD HMD1 ? ? SING CMD HMD2 ? ? SING CMD HMD3 ? ? SING C3D CAD ? ? SING CAD CBD ? ? SING CAD HAD1 ? ? SING CAD HAD2 ? ? SING CBD CGD ? ? SING CBD HBD1 ? ? SING CBD HBD2 ? ? DOUB CGD O1D ? ? SING CGD O2D ? ? SING O2D H2D ? ? stop_ _Mol_thiol_state . _Sequence_homology_query_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 single 'metal coordination' MDCSGCSRPG 1 MET SD Zn(II) 1 ZEM ZN single 'metal coordination' MDCSGCSRPG 3 CYS SG Zn(II) 1 ZEM ZN single 'metal coordination' MDCSGCSRPG 6 CYS SG Zn(II) 1 ZEM ZN 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+Zn-H2O_acidic . . . . . . 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+Zn-H2O_acidic '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 TDW and the pH adjusted to 3.0. The peptide was lyophilized and subsequently (2.0 mg, 2.01 umol) dissolved in DMSO-d6 (450 uL); and a stock solution of ZnCl2 (50 uL, 40.0 mM) in TDW was added, giving a dilution factor of 10 and a final concentration of 4.0 mM. ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $MDCSGCSRPG+Zn-H2O_acidic 4.0 mM 'natural abundance' ZnCl2 4.0 mM 'natural abundance' DMSO 90 % [U-2H] H2O 10 % '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_MDCSGCSRPG+Zn_from_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 7.61 . . 2 1 1 MET HA H 4.32 . . 3 1 1 MET HB2 H 2.28 . . 4 1 1 MET HB3 H 1.92 . . 5 1 1 MET HG2 H 2.46 . . 6 1 1 MET HG3 H 2.46 . . 7 2 2 ASP H H 8.65 . . 8 2 2 ASP HA H 4.55 . . 9 2 2 ASP HB2 H 2.81 . . 10 2 2 ASP HB3 H 2.42 . . 11 3 3 CYS H H 7.42 . . 12 3 3 CYS HA H 4.65 . . 13 3 3 CYS HB2 H 3.06 . . 14 3 3 CYS HB3 H 3.06 . . 15 4 4 SER H H 8.81 . . 16 4 4 SER HA H 4.14 . . 17 4 4 SER HB2 H 3.62 . . 18 4 4 SER HB3 H 3.56 . . 19 5 5 GLY H H 8.76 . . 20 5 5 GLY HA2 H 3.72 . . 21 5 5 GLY HA3 H 3.57 . . 22 6 6 CYS H H 8.33 . . 23 6 6 CYS HA H 4.13 . . 24 6 6 CYS HB2 H 3.67 . . 25 6 6 CYS HB3 H 3.52 . . 26 7 7 SER H H 7.23 . . 27 7 7 SER HA H 4.32 . . 28 7 7 SER HB2 H 3.20 . . 29 7 7 SER HB3 H 3.20 . . 30 8 8 ARG H H 7.11 . . 31 8 8 ARG HA H 4.49 . . 32 8 8 ARG HB2 H 1.64 . . 33 8 8 ARG HB3 H 1.64 . . 34 8 8 ARG HD2 H 3.60 . . 35 8 8 ARG HD3 H 3.60 . . 36 8 8 ARG HE H 7.46 . . 37 8 8 ARG HG2 H 1.52 . . 38 8 8 ARG HG3 H 1.52 . . 39 9 9 PRO HA H 4.23 . . 40 9 9 PRO HB2 H 2.14 . . 41 9 9 PRO HB3 H 1.73 . . 42 9 9 PRO HD2 H 3.84 . . 43 9 9 PRO HD3 H 3.50 . . 44 9 9 PRO HG2 H 1.95 . . 45 9 9 PRO HG3 H 1.86 . . 46 10 10 GLY H H 8.46 . . 47 10 10 GLY HA2 H 3.90 . . 48 10 10 GLY HA3 H 3.47 . . stop_ save_