data_5157 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of a hydrophobic analogue of the winter flounder antifreeze protein ; _BMRB_accession_number 5157 _BMRB_flat_file_name bmr5157.str _Entry_type original _Submission_date 2001-09-24 _Accession_date 2001-09-25 _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 Liepinsh Edvards . . 2 Otting Gottfried . . 3 Harding Margaret M. . 4 Ward Leanne G. . 5 Mackay Joel P. . 6 Haymet A. D.J. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 161 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-07-16 update BMRB 'Updating non-standard residue' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Solution Structure of a Hydrophobic Analogue of the Winter Flounder Antifreeze Protein ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 21845977 _PubMed_ID 11856360 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Liepinsh Edvards . . 2 Otting Gottfried . . 3 Harding Margaret M. . 4 Ward Leanne G. . 5 Mackay Joel P. . 6 Haymet A. D.J. . stop_ _Journal_abbreviation 'Eur. J. Biochem.' _Journal_volume 269 _Journal_issue 4 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1259 _Page_last 1266 _Year 2002 _Details . save_ ####################################### # Cited references within the entry # ####################################### save_ref_1 _Saveframe_category citation _Citation_full ; Haymet, A.D.J., Ward, L.G., Harding, M.M. & Knight, C.A. (1998) Valine substituted winter flounder antifreeze - preservation of ice growth hysteresis, FEBS Lett., 430, 301-306. ; _Citation_title "Valine substituted winter flounder 'antifreeze': preservation of ice growth hysteresis." _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 9688560 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Haymet 'A. D.' D. . 2 Ward 'L. G.' G. . 3 Harding 'M. M.' M. . 4 Knight 'C. A.' A. . stop_ _Journal_abbreviation 'FEBS Lett.' _Journal_name_full 'FEBS letters' _Journal_volume 430 _Journal_issue 3 _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first 301 _Page_last 306 _Year 1998 _Details ; Three mutant polypeptides of the type I 37-residue winter flounder 'antifreeze' protein have been synthesized. All four threonine residues in the native peptide were been mutated to serine, valine and glycine respectively and two additional salt bridges were incorporated into the sequences in order to improve aqueous solubility. The peptides were analyzed by nanoliter osmometry, the 'ice hemisphere' test, the 'crystal habit' test, measurement of ice growth hysteresis and CD spectroscopy. While the valine and serine mutants retain the alpha-helical structure, only the valine mutant retains 'antifreeze' activity similar to that of the native protein. These data show that the threonine hydroxyl groups do not play a crucial role in the accumulation of the native 'antifreeze' protein at the ice/water interface and the inhibition of ice growth below the equilibrium melting temperature. ; save_ ################################## # Molecular system description # ################################## save_system_type_1_AFP_mutant _Saveframe_category molecular_system _Mol_system_name 'Antifreeze protein type 1 mutant' _Abbreviation_common 'type 1 AFP mutant' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'type 1 AFP mutant' $VVVV2KE stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'not present' loop_ _Biological_function 'lowers melting point of water' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_VVVV2KE _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'antifreeze protein type 1 mutant' _Abbreviation_common VVVV2KE _Molecular_mass 3464 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 37 _Mol_residue_sequence ; DVASDAKAAAELVAANAKAA AELVAANAKAAAEAVAX ; loop_ _Residue_seq_code _Residue_label 1 ASP 2 VAL 3 ALA 4 SER 5 ASP 6 ALA 7 LYS 8 ALA 9 ALA 10 ALA 11 GLU 12 LEU 13 VAL 14 ALA 15 ALA 16 ASN 17 ALA 18 LYS 19 ALA 20 ALA 21 ALA 22 GLU 23 LEU 24 VAL 25 ALA 26 ALA 27 ASN 28 ALA 29 LYS 30 ALA 31 ALA 32 ALA 33 GLU 34 ALA 35 VAL 36 ALA 37 AAR stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2014-05-25 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 1J5B "Solution Structure Of A Hydrophobic Analogue Of The Winter Flounder Antifreeze Protein" 97.30 38 100.00 100.00 2.28e-08 stop_ save_ ###################### # Polymer residues # ###################### save_chem_comp_AAR _Saveframe_category polymer_residue _Mol_type 'L-peptide linking' _Name_common ARGININEAMIDE _BMRB_code . _PDB_code AAR _Standard_residue_derivative . _Molecular_mass 174.224 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Thu Jul 21 10:47:26 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? 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 . 1 . ? C C C . 0 . ? O O O . 0 . ? NT NT N . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG2 HG2 H . 0 . ? HG3 HG3 H . 0 . ? HD2 HD2 H . 0 . ? HD3 HD3 H . 0 . ? HE HE H . 0 . ? HH11 HH11 H . 0 . ? HH12 HH12 H . 0 . ? HH21 HH21 H . 0 . ? HH22 HH22 H . 0 . ? HNT1 HNT1 H . 0 . ? HNT2 HNT2 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 N CA ? ? SING N H ? ? SING N H2 ? ? SING CA CB ? ? SING CA C ? ? SING CA HA ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG CD ? ? SING CG HG2 ? ? SING CG HG3 ? ? SING CD NE ? ? SING CD HD2 ? ? SING CD HD3 ? ? SING NE CZ ? ? SING NE HE ? ? SING CZ NH1 ? ? DOUB CZ NH2 ? ? SING NH1 HH11 ? ? SING NH1 HH12 ? ? SING NH2 HH21 ? ? SING NH2 HH22 ? ? DOUB C O ? ? SING C NT ? ? SING NT HNT1 ? ? SING NT HNT2 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $VVVV2KE 'winter flounder' 8265 Eukaryota Metazoa Pseudopleuronectes americanus 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 $VVVV2KE 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $VVVV2KE 11 mM . NaCl 100 mM . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $VVVV2KE 2 mM . NaCl 100 mM . stop_ save_ ############################ # Computer software used # ############################ save_PROSA _Saveframe_category software _Name PROSA _Version 2.6 loop_ _Task 'spectra processing' stop_ _Details . save_ save_XEASY _Saveframe_category software _Name XEASY _Version 2.5 loop_ _Task 'spectral analysis' stop_ _Details . save_ save_DYANA _Saveframe_category software _Name DYANA _Version 2.6 loop_ _Task 'structure calculation' stop_ _Details . save_ save_OPAL _Saveframe_category software _Name OPAL _Version 2.2 loop_ _Task 'structure refinement' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DMX _Field_strength 600 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model Unity-INOVA _Field_strength 800 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label . save_ save_2D_ROESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D ROESY' _Sample_label . save_ save_2D_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label . save_ save_2D_DQF-COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label . save_ save_NMR_applied_experiment _Saveframe_category NMR_applied_experiment _Experiment_name . _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D ROESY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_ex-cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 4.9 0.2 n/a temperature 288 1 K 'ionic strength' 0.1 0.02 M stop_ save_ save_ex-cond_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7.0 0.2 n/a temperature 283 1 K 'ionic strength' 0.1 0.02 M stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _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 H2O H 1 protons ppm 0.00 internal direct cylindrical internal . 1.0 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_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_2 stop_ _Sample_conditions_label $ex-cond_2 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'type 1 AFP mutant' _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 ASP HA H 4.176 0.01 1 2 . 1 ASP HB2 H 2.854 0.01 2 3 . 1 ASP HB3 H 3.024 0.01 2 4 . 2 VAL H H 8.455 0.01 1 5 . 2 VAL HA H 3.912 0.01 1 6 . 2 VAL HB H 2.049 0.01 1 7 . 2 VAL HG1 H 0.960 0.01 1 8 . 2 VAL HG2 H 1.019 0.01 1 9 . 3 ALA H H 8.242 0.01 1 10 . 3 ALA HA H 4.244 0.01 1 11 . 3 ALA HB H 1.430 0.01 1 12 . 4 SER H H 8.678 0.01 1 13 . 4 SER HA H 4.236 0.01 1 14 . 4 SER HB2 H 3.897 0.01 2 15 . 4 SER HB3 H 4.000 0.01 2 16 . 5 ASP H H 8.456 0.01 1 17 . 5 ASP HA H 4.489 0.01 1 18 . 5 ASP HB3 H 2.673 0.01 1 19 . 5 ASP HB2 H 2.795 0.01 1 20 . 6 ALA H H 8.243 0.01 1 21 . 6 ALA HA H 4.219 0.01 1 22 . 6 ALA HB H 1.483 0.01 1 23 . 7 LYS H H 8.059 0.01 1 24 . 7 LYS HA H 4.130 0.01 1 25 . 7 LYS HB2 H 1.886 0.01 2 26 . 7 LYS HB3 H 1.922 0.01 2 27 . 7 LYS HG2 H 1.363 0.01 2 28 . 7 LYS HG3 H 1.491 0.01 2 29 . 8 ALA H H 8.037 0.01 1 30 . 8 ALA HA H 4.192 0.01 1 31 . 8 ALA HB H 1.496 0.01 1 32 . 9 ALA H H 8.146 0.01 1 33 . 9 ALA HA H 4.173 0.01 1 34 . 9 ALA HB H 1.481 0.01 1 35 . 10 ALA H H 8.006 0.01 1 36 . 10 ALA HA H 4.180 0.01 1 37 . 10 ALA HB H 1.520 0.01 1 38 . 11 GLU H H 8.302 0.01 1 39 . 11 GLU HA H 4.074 0.01 1 40 . 11 GLU HB3 H 2.028 0.01 1 41 . 11 GLU HB2 H 2.164 0.01 1 42 . 11 GLU HG2 H 2.267 0.01 2 43 . 11 GLU HG3 H 2.500 0.01 2 44 . 12 LEU H H 7.823 0.01 1 45 . 12 LEU HA H 4.263 0.01 1 46 . 12 LEU HB2 H 1.704 0.01 1 47 . 12 LEU HB3 H 1.842 0.01 1 48 . 12 LEU HG H 1.655 0.01 1 49 . 12 LEU HD1 H 0.895 0.01 1 50 . 12 LEU HD2 H 0.928 0.01 1 51 . 13 VAL H H 7.750 0.01 1 52 . 13 VAL HA H 3.703 0.01 1 53 . 13 VAL HB H 2.142 0.01 1 54 . 13 VAL HG1 H 0.958 0.01 1 55 . 13 VAL HG2 H 1.087 0.01 1 56 . 14 ALA H H 7.907 0.01 1 57 . 14 ALA HA H 4.215 0.01 1 58 . 14 ALA HB H 1.476 0.01 1 59 . 15 ALA H H 8.402 0.01 1 60 . 15 ALA HA H 4.175 0.01 1 61 . 15 ALA HB H 1.522 0.01 1 62 . 16 ASN H H 8.618 0.01 1 63 . 16 ASN HA H 4.547 0.01 1 64 . 16 ASN HB3 H 2.804 0.01 1 65 . 16 ASN HB2 H 2.917 0.01 1 66 . 16 ASN HD22 H 6.877 0.01 1 67 . 16 ASN HD21 H 7.684 0.01 1 68 . 17 ALA H H 8.199 0.01 1 69 . 17 ALA HA H 4.236 0.01 1 70 . 17 ALA HB H 1.498 0.01 1 71 . 18 LYS H H 8.086 0.01 1 72 . 18 LYS HA H 4.136 0.01 1 73 . 18 LYS HB2 H 1.894 0.01 2 74 . 18 LYS HB3 H 1.919 0.01 2 75 . 18 LYS HG2 H 1.368 0.01 2 76 . 18 LYS HG3 H 1.498 0.01 2 77 . 19 ALA H H 7.994 0.01 1 78 . 19 ALA HA H 4.199 0.01 1 79 . 19 ALA HB H 1.489 0.01 1 80 . 20 ALA H H 8.144 0.01 1 81 . 20 ALA HA H 4.180 0.01 1 82 . 20 ALA HB H 1.495 0.01 1 83 . 21 ALA H H 7.981 0.01 1 84 . 21 ALA HA H 4.180 0.01 1 85 . 21 ALA HB H 1.525 0.01 1 86 . 22 GLU H H 8.303 0.01 1 87 . 22 GLU HA H 4.079 0.01 1 88 . 22 GLU HB3 H 2.023 0.01 1 89 . 22 GLU HB2 H 2.169 0.01 1 90 . 22 GLU HG2 H 2.257 0.01 2 91 . 22 GLU HG3 H 2.511 0.01 2 92 . 23 LEU H H 7.817 0.01 1 93 . 23 LEU HA H 4.265 0.01 1 94 . 23 LEU HB2 H 1.703 0.01 1 95 . 23 LEU HB3 H 1.841 0.01 1 96 . 23 LEU HG H 1.654 0.01 1 97 . 23 LEU HD1 H 0.895 0.01 1 98 . 23 LEU HD2 H 0.929 0.01 1 99 . 24 VAL H H 7.753 0.01 1 100 . 24 VAL HA H 3.697 0.01 1 101 . 24 VAL HB H 2.144 0.01 1 102 . 24 VAL HG1 H 0.960 0.01 1 103 . 24 VAL HG2 H 1.088 0.01 1 104 . 25 ALA H H 7.912 0.01 1 105 . 25 ALA HA H 4.218 0.01 1 106 . 25 ALA HB H 1.478 0.01 1 107 . 26 ALA H H 8.431 0.01 1 108 . 26 ALA HA H 4.181 0.01 1 109 . 26 ALA HB H 1.529 0.01 1 110 . 27 ASN H H 8.666 0.01 1 111 . 27 ASN HA H 4.551 0.01 1 112 . 27 ASN HB3 H 2.793 0.01 1 113 . 27 ASN HB2 H 2.937 0.01 1 114 . 27 ASN HD22 H 6.873 0.01 1 115 . 27 ASN HD21 H 7.686 0.01 1 116 . 28 ALA H H 8.237 0.01 1 117 . 28 ALA HA H 4.245 0.01 1 118 . 28 ALA HB H 1.512 0.01 1 119 . 29 LYS H H 8.119 0.01 1 120 . 29 LYS HA H 4.138 0.01 1 121 . 29 LYS HB2 H 1.906 0.01 2 122 . 29 LYS HB3 H 1.944 0.01 2 123 . 29 LYS HG2 H 1.365 0.01 2 124 . 29 LYS HG3 H 1.488 0.01 2 125 . 30 ALA H H 7.995 0.01 1 126 . 30 ALA HA H 4.194 0.01 1 127 . 30 ALA HB H 1.507 0.01 1 128 . 31 ALA H H 8.131 0.01 1 129 . 31 ALA HA H 4.184 0.01 1 130 . 31 ALA HB H 1.467 0.01 1 131 . 32 ALA H H 7.941 0.01 1 132 . 32 ALA HA H 4.183 0.01 1 133 . 32 ALA HB H 1.495 0.01 1 134 . 33 GLU H H 8.204 0.01 1 135 . 33 GLU HA H 4.075 0.01 1 136 . 33 GLU HB3 H 2.007 0.01 1 137 . 33 GLU HB2 H 2.088 0.01 1 138 . 33 GLU HG2 H 2.240 0.01 2 139 . 33 GLU HG3 H 2.458 0.01 2 140 . 34 ALA H H 7.861 0.01 1 141 . 34 ALA HA H 4.147 0.01 1 142 . 34 ALA HB H 1.469 0.01 1 143 . 35 VAL H H 7.756 0.01 1 144 . 35 VAL HA H 3.821 0.01 1 145 . 35 VAL HB H 2.104 0.01 1 146 . 35 VAL HG1 H 0.928 0.01 1 147 . 35 VAL HG2 H 1.031 0.01 1 148 . 36 ALA H H 7.925 0.01 1 149 . 36 ALA HA H 4.180 0.01 1 150 . 36 ALA HB H 1.434 0.01 1 151 . 37 AAR H H 7.896 0.01 1 152 . 37 AAR HA H 4.179 0.01 1 153 . 37 AAR HB2 H 1.840 0.01 1 154 . 37 AAR HB3 H 1.870 0.01 1 155 . 37 AAR HG2 H 1.649 0.01 2 156 . 37 AAR HG3 H 1.744 0.01 2 157 . 37 AAR HD2 H 3.168 0.01 2 158 . 37 AAR HD3 H 3.205 0.01 2 159 . 37 AAR HE H 7.242 0.01 1 160 . 37 AAR HT1 H 7.467 0.01 1 161 . 37 AAR HT2 H 7.406 0.01 1 stop_ save_