data_17669 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; 1H Chemical Shift Assignments and structure of Trp-Cage mini-protein with D-amino acid ; _BMRB_accession_number 17669 _BMRB_flat_file_name bmr17669.str _Entry_type original _Submission_date 2011-05-27 _Accession_date 2011-05-27 _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 Granillo Agustina Rodriguez . 2 Annavarapu Srinivas . . 3 Zhang Lei . . 4 Koder Ronald . . 5 Nanda Vikas . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 125 "15N chemical shifts" 1 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-08-08 update BMRB 'update entry citation' 2011-06-24 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title 'Computational design of thermostabilizing D-amino acid substitutions.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 21978298 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Rodriguez-Granillo Agustina . . 2 Annavarapu Srinivas . . 3 Zhang Lei . . 4 Koder Ronald L. . 5 Nanda Vikas . . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_name_full 'Journal of the American Chemical Society' _Journal_volume 133 _Journal_issue 46 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 18750 _Page_last 18759 _Year 2011 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Trp-Cage mini-protein with D-amino acid' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'Trp-Cage mini-protein with D-amino acid' $Trp-Cage_mini-protein 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_Trp-Cage_mini-protein _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common Trp-Cage_mini-protein _Molecular_mass 2271.578 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 20 _Mol_residue_sequence ; NLYIQWLKDXGPSSGRPPPS ; loop_ _Residue_seq_code _Residue_label 1 ASN 2 LEU 3 TYR 4 ILE 5 GLN 6 TRP 7 LEU 8 LYS 9 ASP 10 GND 11 GLY 12 PRO 13 SER 14 SER 15 GLY 16 ARG 17 PRO 18 PRO 19 PRO 20 SER stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2014-12-21 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 PDB 2LDJ "1h Chemical Shift Assignments And Structure Of Trp-Cage Mini-Protein With D-Amino Acid" 100.00 20 100.00 100.00 1.18e-03 stop_ save_ ###################### # Polymer residues # ###################### save_chem_comp_GND _Saveframe_category polymer_residue _Mol_type 'L-peptide linking' _Name_common '2-AMINO-5-GUANIDINO-PENTANOIC ACID' _BMRB_code . _PDB_code GND _Standard_residue_derivative . _Molecular_mass 175.209 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Wed Jun 15 17:53:56 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons CA CA C . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? CD CD C . 0 . ? NE NE N . 0 . ? CZ CZ C . 0 . ? NH1 NH1 N . 0 . ? NH2 NH2 N . 0 . ? C C C . 0 . ? OXT OXT O . 0 . ? O O O . 0 . ? N N N . 1 . ? HA HA H . 0 . ? HB1 HB1 H . 0 . ? HB2 HB2 H . 0 . ? HG1 HG1 H . 0 . ? HG2 HG2 H . 0 . ? HD1 HD1 H . 0 . ? HD2 HD2 H . 0 . ? HE HE H . 0 . ? HH11 HH11 H . 0 . ? HH21 HH21 H . 0 . ? HH22 HH22 H . 0 . ? HXT HXT H . 0 . ? HN1 HN1 H . 0 . ? HN2 HN2 H . 0 . ? HN3 HN3 H . 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 CA CB ? ? SING CA C ? ? SING CA N ? ? SING CA HA ? ? SING CB CG ? ? SING CB HB1 ? ? SING CB HB2 ? ? SING CG CD ? ? SING CG HG1 ? ? SING CG HG2 ? ? SING CD NE ? ? SING CD HD1 ? ? SING CD HD2 ? ? SING NE CZ ? ? SING NE HE ? ? DOUB CZ NH1 ? ? SING CZ NH2 ? ? SING NH1 HH11 ? ? SING NH2 HH21 ? ? SING NH2 HH22 ? ? SING C OXT ? ? DOUB C O ? ? SING OXT HXT ? ? SING N HN1 ? ? SING N HN2 ? ? SING N HN3 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $Trp-Cage_mini-protein . . . . . . 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 $Trp-Cage_mini-protein 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Trp-Cage_mini-protein 2.5 mM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Trp-Cage_mini-protein 1.5 mM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_ARIA _Saveframe_category software _Name ARIA _Version 2.2 loop_ _Vendor _Address _Electronic_address 'Linge, O'Donoghue and Nilges' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_CNS _Saveframe_category software _Name CNS _Version . loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _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-13C_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_2 save_ save_2D_1H-15N_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 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' 0.05 . M pH 7 . pH pressure 1 . atm temperature 278 . 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 . . . 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 NOESY' '2D 1H-1H TOCSY' '2D 1H-13C HSQC' '2D 1H-15N HSQC' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'Trp-Cage mini-protein with D-amino acid' _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 ASN HA H 4.316 0.005 1 2 1 1 ASN HB2 H 3.216 0.004 2 3 1 1 ASN HB3 H 3.024 0.008 2 4 1 1 ASN HD21 H 7.949 0.001 2 5 1 1 ASN HD22 H 7.3 0.002 2 6 2 2 LEU H H 9.086 0.001 1 7 2 2 LEU HA H 4.194 0.005 1 8 2 2 LEU HB2 H 1.803 0.004 2 9 2 2 LEU HB3 H 1.437 0.002 2 10 2 2 LEU HG H 1.788 0.007 1 11 2 2 LEU HD1 H 0.948 0.002 2 12 2 2 LEU HD2 H 0.899 0.005 2 13 3 3 TYR H H 8.65 0.001 1 14 3 3 TYR HA H 4.056 0.001 1 15 3 3 TYR HB2 H 3.096 0.001 2 16 3 3 TYR HB3 H 3.097 0.001 2 17 3 3 TYR HD1 H 6.991 0.003 3 18 3 3 TYR HD2 H 6.991 0.003 3 19 3 3 TYR HE1 H 6.784 0.011 3 20 3 3 TYR HE2 H 6.798 0.003 3 21 4 4 ILE H H 8.19 0.001 1 22 4 4 ILE HA H 3.721 0.002 1 23 4 4 ILE HB H 1.965 0.003 1 24 4 4 ILE HG12 H 1.678 0.003 2 25 4 4 ILE HG13 H 1.433 0.003 2 26 4 4 ILE HG2 H 0.938 0.003 1 27 4 4 ILE HD1 H 0.905 0.005 1 28 5 5 GLN H H 7.877 0.001 1 29 5 5 GLN HA H 3.871 0.002 1 30 5 5 GLN HB2 H 2.062 0.002 2 31 5 5 GLN HB3 H 2.181 0.002 2 32 5 5 GLN HG2 H 2.398 0.001 2 33 5 5 GLN HG3 H 2.398 0.001 2 34 5 5 GLN HE21 H 7.785 0.001 2 35 5 5 GLN HE22 H 7.043 0.001 2 36 6 6 TRP H H 8.045 0.001 1 37 6 6 TRP HA H 4.186 0.005 1 38 6 6 TRP HB2 H 3.118 0.003 2 39 6 6 TRP HB3 H 3.554 0.005 2 40 6 6 TRP HD1 H 6.954 0.001 1 41 6 6 TRP HE1 H 9.67 0.001 1 42 6 6 TRP HE3 H 7.03 0.004 1 43 6 6 TRP HZ2 H 7.146 0.004 1 44 6 6 TRP HZ3 H 7.1 0.002 1 45 6 6 TRP HH2 H 7.18 0.003 1 46 7 7 LEU H H 8.329 0.001 1 47 7 7 LEU HA H 3.323 0.001 1 48 7 7 LEU HB2 H 1.917 0.004 2 49 7 7 LEU HB3 H 1.294 0.002 2 50 7 7 LEU HG H 1.559 0.002 1 51 7 7 LEU HD1 H 0.906 0.001 2 52 7 7 LEU HD2 H 0.816 0.002 2 53 8 8 LYS H H 8.294 0.001 1 54 8 8 LYS HA H 3.879 0.002 1 55 8 8 LYS HB2 H 1.892 0.003 2 56 8 8 LYS HB3 H 1.897 0.001 2 57 8 8 LYS HG2 H 1.513 0.005 2 58 8 8 LYS HG3 H 1.412 0.003 2 59 8 8 LYS HD2 H 1.598 0.007 2 60 8 8 LYS HD3 H 1.598 0.007 2 61 8 8 LYS HE2 H 2.902 0.006 2 62 8 8 LYS HE3 H 2.904 0.001 2 63 8 8 LYS HZ H 7.589 0.001 1 64 9 9 ASP H H 8.001 0.001 1 65 9 9 ASP HA H 4.506 0.002 1 66 9 9 ASP HB2 H 2.921 0.014 2 67 9 9 ASP HB3 H 2.772 0.004 2 68 10 10 GND HA H 4.144 0.002 1 69 10 10 GND HB1 H 1.62 0.003 2 70 10 10 GND HB2 H 2.204 0.005 2 71 10 10 GND HG2 H 2.092 0.003 2 72 10 10 GND HH21 H 7.472 0.001 2 73 10 10 GND NH1 N 7.314 0.001 1 74 10 10 GND HH22 H 6.773 0.002 2 75 10 10 GND HG1 H 2.212 0.003 2 76 11 11 GLY H H 8.51 0.001 1 77 11 11 GLY HA2 H 0.631 0.004 2 78 11 11 GLY HA3 H 3.113 0.003 2 79 12 12 PRO HA H 4.623 0.003 1 80 12 12 PRO HB2 H 2.043 0.003 2 81 12 12 PRO HG2 H 2.145 0.001 2 82 12 12 PRO HG3 H 2.145 0.001 2 83 12 12 PRO HD2 H 3.787 0.002 2 84 12 12 PRO HD3 H 3.481 0.001 2 85 13 13 SER H H 7.708 0.001 1 86 13 13 SER HA H 4.44 0.007 1 87 13 13 SER HB2 H 3.866 0.001 2 88 13 13 SER HB3 H 3.912 0.003 2 89 14 14 SER H H 8.193 0.001 1 90 14 14 SER HA H 4.064 0.005 1 91 14 14 SER HB2 H 3.383 0.004 2 92 14 14 SER HB3 H 3.782 0.003 2 93 15 15 GLY H H 7.943 0.001 1 94 15 15 GLY HA2 H 3.757 0.001 2 95 15 15 GLY HA3 H 4.236 0.001 2 96 16 16 ARG H H 8.097 0.001 1 97 16 16 ARG HB2 H 1.838 0.005 2 98 16 16 ARG HB3 H 1.611 0.001 2 99 16 16 ARG HG2 H 1.769 0.006 2 100 16 16 ARG HG3 H 1.74 0.005 2 101 16 16 ARG HD2 H 3.185 0.005 2 102 16 16 ARG HD3 H 3.255 0.002 2 103 16 16 ARG HE H 7.647 0.001 1 104 17 17 PRO HA H 4.705 0.001 1 105 17 17 PRO HB2 H 1.744 0.009 2 106 17 17 PRO HB3 H 2.282 0.006 2 107 17 17 PRO HG2 H 1.963 0.003 2 108 17 17 PRO HG3 H 1.963 0.003 2 109 17 17 PRO HD2 H 3.623 0.001 2 110 17 17 PRO HD3 H 3.818 0.004 2 111 18 18 PRO HA H 2.437 0.002 1 112 18 18 PRO HB2 H 1.278 0.001 2 113 18 18 PRO HB3 H 0.291 0.003 2 114 18 18 PRO HG2 H 1.693 0.001 2 115 18 18 PRO HG3 H 1.646 0.003 2 116 18 18 PRO HD2 H 3.482 0.004 2 117 18 18 PRO HD3 H 3.473 0.003 2 118 19 19 PRO HA H 4.309 0.005 1 119 19 19 PRO HB2 H 1.951 0.007 2 120 19 19 PRO HB3 H 2.179 0.003 2 121 19 19 PRO HG2 H 1.749 0.003 2 122 19 19 PRO HG3 H 1.81 0.004 2 123 19 19 PRO HD2 H 2.913 0.004 2 124 19 19 PRO HD3 H 3.103 0.004 2 125 20 20 SER H H 8.031 0.004 1 126 20 20 SER HA H 4.157 0.004 1 stop_ save_