data_15107 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR structure of D4P/K7G mutant of GPM12 ; _BMRB_accession_number 15107 _BMRB_flat_file_name bmr15107.str _Entry_type new _Submission_date 2007-01-22 _Accession_date 2007-01-22 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Terada T. . . 2 Satoh D. . . 3 Mikawa T. . . 4 Ito Y. . . 5 Shimizu K. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 47 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-06-25 original author . stop_ save_ ############################# # Citation for this entry # ############################# save_citations _Saveframe_category entry_citation _Citation_title 'Understanding the roles of amino acid residues in tertiary structure formation of chignolin by using molecular dynamics simulation' _Citation_status published _Citation_type journal _PubMed_ID 18473359 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Terada T. . . 2 Satoh D. . . 3 Mikawa T. . . 4 Ito Y. . . 5 Shimizu K. . . stop_ _Journal_abbreviation Proteins _Journal_volume . _Journal_issue . _Journal_CSD 0353 _Page_first . _Page_last . _Year 2008 save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name GPM12 loop_ _Mol_system_component_name _Mol_label GPM12 $GPM12 stop_ _System_physical_state native _System_oligomer_state ? _System_paramagnetic no save_ ######################## # Monomeric polymers # ######################## save_GPM12 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common GPM12 _Mol_thiol_state 'not present' ############################## # Polymer residue sequence # ############################## _Residue_count 10 _Mol_residue_sequence GYDPATGTFG loop_ _Residue_seq_code _Residue_label 1 GLY 2 TYR 3 ASP 4 PRO 5 ALA 6 THR 7 GLY 8 THR 9 PHE 10 GLY stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $GPM12 . . . . . . 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 _Details $GPM12 'chemical synthesis' . . . . ? 'CHEMICAL PEPTIDE SYNTHESIS' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample _Saveframe_category sample _Sample_type solution _Details '2mM GPM12(D4P/K7G)' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $GPM12 2 mM 'natural abundance' 'sodium phosphate' 20 mM 'natural abundance' D2O 10 % [U-2H] H2O 90 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_XWINNMR _Saveframe_category software _Name XWINNMR _Version 3.5 loop_ _Vendor _Address _Electronic_address 'Bruker BioSpin Corporation' . . stop_ loop_ _Task collection stop_ save_ save_AZARA _Saveframe_category software _Name AZARA _Version 2.7 loop_ _Vendor _Address _Electronic_address 'Wayne Boucher' . . stop_ loop_ _Task processing stop_ save_ save_ANSIG _Saveframe_category software _Name ANSIG _Version '3.3 for OpenGL version 1.0.6' loop_ _Vendor _Address _Electronic_address 'Per Kraulis, Takeshi Nishimura' . . stop_ loop_ _Task 'data analysis' stop_ save_ save_CNS _Saveframe_category software _Name CNS _Version 1.1 loop_ _Vendor _Address _Electronic_address 'Axel T.Brunger et al.' . . stop_ loop_ _Task 'structure solution' refinement stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 600 save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample save_ save_2D_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label $sample save_ save_2D_ROESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D ROESY' _Sample_label $sample save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 20 . mM pH 5.5 . pH pressure 1 . atm temperature 277 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference 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 water H 1 protons ppm 5.09 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_1 _Saveframe_category assigned_chemical_shifts loop_ _Experiment_label '2D TOCSY' stop_ loop_ _Sample_label $sample stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name GPM12 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 GLY HA2 H 3.88 0.02 1 2 1 1 GLY HA3 H 3.88 0.02 1 3 2 2 TYR H H 8.89 0.02 1 4 2 2 TYR HA H 4.48 0.02 1 5 2 2 TYR HB2 H 2.97 0.02 1 6 2 2 TYR HB3 H 2.83 0.02 1 7 2 2 TYR HD1 H 6.86 0.02 1 8 2 2 TYR HD2 H 6.86 0.02 1 9 2 2 TYR HE1 H 6.74 0.02 1 10 2 2 TYR HE2 H 6.74 0.02 1 11 3 3 ASP H H 8.46 0.02 1 12 3 3 ASP HA H 4.98 0.02 1 13 3 3 ASP HB2 H 2.62 0.02 1 14 3 3 ASP HB3 H 2.99 0.02 1 15 4 4 PRO HA H 4.21 0.02 1 16 4 4 PRO HB2 H 2.05 0.02 1 17 4 4 PRO HB3 H 2.05 0.02 1 18 4 4 PRO HG2 H 2.39 0.02 1 19 4 4 PRO HG3 H 2.39 0.02 1 20 4 4 PRO HD2 H 3.82 0.02 1 21 4 4 PRO HD3 H 3.62 0.02 1 22 5 5 ALA H H 8.21 0.02 1 23 5 5 ALA HA H 4.31 0.02 1 24 5 5 ALA HB H 1.48 0.02 1 25 6 6 THR H H 7.70 0.02 1 26 6 6 THR HA H 4.40 0.02 1 27 6 6 THR HB H 4.32 0.02 1 28 6 6 THR HG2 H 1.20 0.02 1 29 7 7 GLY H H 8.46 0.02 1 30 7 7 GLY HA2 H 3.95 0.02 1 31 7 7 GLY HA3 H 4.07 0.02 1 32 8 8 THR H H 7.84 0.02 1 33 8 8 THR HA H 4.47 0.02 1 34 8 8 THR HB H 4.21 0.02 1 35 8 8 THR HG2 H 1.16 0.02 1 36 9 9 PHE H H 8.69 0.02 1 37 9 9 PHE HA H 4.80 0.02 1 38 9 9 PHE HB2 H 3.26 0.02 1 39 9 9 PHE HB3 H 3.03 0.02 1 40 9 9 PHE HD1 H 7.32 0.02 1 41 9 9 PHE HD2 H 7.32 0.02 1 42 9 9 PHE HE1 H 7.40 0.02 1 43 9 9 PHE HE2 H 7.40 0.02 1 44 9 9 PHE HZ H 7.32 0.02 1 45 10 10 GLY H H 8.25 0.02 1 46 10 10 GLY HA2 H 3.92 0.02 1 47 10 10 GLY HA3 H 3.92 0.02 1 stop_ save_