data_15946 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of a paralog-specific Mena binder by NMR ; _BMRB_accession_number 15946 _BMRB_flat_file_name bmr15946.str _Entry_type original _Submission_date 2008-09-09 _Accession_date 2008-09-09 _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 Link Nina M. . 2 Hunke Cornelia . . 3 Eichler Jutta . . 4 Bayer Peter . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 174 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-06-02 update BMRB 'edit assembly name' 2009-06-01 update BMRB 'complete entry citation' 2009-04-04 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_citations_1 _Saveframe_category entry_citation _Citation_full . _Citation_title 'The solution structure of pGolemi, a high affinity Mena EVH1 binding miniature protein, suggests explanations for paralog-specific binding to Ena/VASP homology (EVH) 1 domains' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 19284291 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Link Nina M. . 2 Hunke Cornelia . . 3 Mueller Jonathan W. . 4 Eichler Jutta . . 5 Bayer Peter . . stop_ _Journal_abbreviation 'Biol. Chem.' _Journal_volume 390 _Journal_issue 5-6 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 417 _Page_last 26 _Year 2009 _Details . loop_ _Keyword 'Ligand Design' 'NMR spectroscopy' Peptides 'Structure Elucidation' stop_ save_ ####################################### # Cited references within the entry # ####################################### save_citations_2 _Saveframe_category citation _Citation_full . _Citation_title 'Miniature protein ligands for EVH1 domains: interplay between affinity, specificity, and cell motility' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 14709031 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Golemi-Kotra Dasantila . . 2 Mahaffy Rachel . . 3 Footer Matthew J. . 4 Holtzman Jennifer H. . 5 Pollard Thomas D. . 6 Theriot Julie A. . 7 Schepartz Alanna . . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_name_full . _Journal_volume 126 _Journal_issue 1 _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 4 _Page_last 5 _Year 2004 _Details . save_ save_citations_3 _Saveframe_category citation _Citation_full . _Citation_title 'Miniature Protein Ligands for EVH1 Domains: Interplay between Affinity, Specificity, and Cell Motility' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 17973491 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Holtzman Jennifer H. . 2 Woronowicz Kamil . . 3 Golemi-Kotra Dasantila . . 4 Schepartz Alanna . . stop_ _Journal_abbreviation Biochemistry _Journal_name_full . _Journal_volume 46 _Journal_issue 47 _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 13541 _Page_last 13553 _Year 2007 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name pGolemi _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label pGolemi $pGolemi 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_pGolemi _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common pGolemi _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 30 _Mol_residue_sequence ; PFPPTPPGEEAPVEDLIRFY NDLQQYLNVV ; loop_ _Residue_seq_code _Residue_label 1 PRO 2 PHE 3 PRO 4 PRO 5 THR 6 PRO 7 PRO 8 GLY 9 GLU 10 GLU 11 ALA 12 PRO 13 VAL 14 GLU 15 ASP 16 LEU 17 ILE 18 ARG 19 PHE 20 TYR 21 ASN 22 ASP 23 LEU 24 GLN 25 GLN 26 TYR 27 LEU 28 ASN 29 VAL 30 VAL stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-02-05 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 2H3S "Cis-Azobenzene-Avian Pancreatic Polypeptide Bound To Dpc Micelles" 63.33 25 100.00 100.00 1.79e-03 PDB 2H3T "Trans-(4-Aminomethyl)phenylazobenzoic Acid-App Bound To Dpc Micelles" 63.33 25 100.00 100.00 1.79e-03 PDB 2H4B "Cis-4-Aminomethylphenylazobenzoic Acid-Avian Pancreatic Polypeptide" 63.33 25 100.00 100.00 1.79e-03 PDB 2K76 "Solution Structure Of A Paralog-Specific Mena Binder By Nmr" 100.00 30 100.00 100.00 1.85e-11 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $pGolemi . . . . . . 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 $pGolemi 'chemical synthesis' . . . . . 'solid-phase peptide synthesis' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '45mM phosphate buffer NA' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $pGolemi 1 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' 'phosphate buffer' 45 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_Auremol _Saveframe_category software _Name Auremol _Version 2.0 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ save_X-PLOR_NIH _Saveframe_category software _Name X-PLOR_NIH _Version 2.18 loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'structure solution' refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 700 _Details 'equipped with Cryoprobe' save_ ############################# # NMR applied experiments # ############################# save_COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name COSY _Sample_label $sample_1 save_ save_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _Sample_label $sample_1 save_ save_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _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' 45 . mM pH 7.0 . pH pressure 1 . atm temperature 298 . 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 water H 1 protons ppm 4.695 internal direct . . . 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_assigned_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label TOCSY NOESY stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name pGolemi _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 PRO HA H 4.236 . 5 2 1 1 PRO HB2 H 1.701 . 5 3 1 1 PRO HB3 H 1.701 . 2 4 1 1 PRO HD2 H 3.398 . 5 5 1 1 PRO HD3 H 3.398 . 2 6 1 1 PRO HG2 H 1.736 . 5 7 1 1 PRO HG3 H 1.736 . 2 8 2 2 PHE H H 8.049 . 1 9 2 2 PHE HA H 4.745 . 1 10 2 2 PHE HB2 H 2.962 . 1 11 2 2 PHE HB3 H 2.689 . 1 12 2 2 PHE HD1 H 7.111 . 3 13 2 2 PHE HD2 H 7.111 . 3 14 2 2 PHE HE1 H 7.104 . 3 15 2 2 PHE HE2 H 7.104 . 3 16 3 3 PRO HD2 H 3.507 . 2 17 3 3 PRO HD3 H 3.377 . 2 18 4 4 PRO HA H 4.386 . 1 19 4 4 PRO HB2 H 2.182 . 2 20 4 4 PRO HB3 H 2.182 . 2 21 4 4 PRO HG2 H 1.908 . 2 22 4 4 PRO HG3 H 1.908 . 2 23 5 5 THR H H 8.402 . 1 24 5 5 THR HA H 4.339 . 1 25 5 5 THR HB H 3.807 . 1 26 5 5 THR HG2 H 1.072 . 1 27 6 6 PRO HA H 3.810 . 1 28 6 6 PRO HB2 H 1.564 . 2 29 6 6 PRO HB3 H 1.564 . 2 30 6 6 PRO HD2 H 3.807 . 2 31 6 6 PRO HD3 H 3.807 . 2 32 6 6 PRO HG2 H 1.783 . 2 33 6 6 PRO HG3 H 1.674 . 2 34 7 7 PRO HA H 4.236 . 5 35 7 7 PRO HB2 H 1.701 . 5 36 7 7 PRO HB3 H 1.701 . 2 37 7 7 PRO HD2 H 3.398 . 5 38 7 7 PRO HD3 H 3.398 . 2 39 7 7 PRO HG2 H 1.736 . 5 40 7 7 PRO HG3 H 1.736 . 2 41 8 8 GLY H H 8.174 . 1 42 8 8 GLY HA2 H 3.849 . 2 43 8 8 GLY HA3 H 3.771 . 2 44 9 9 GLU H H 8.338 . 1 45 9 9 GLU HA H 3.877 . 1 46 9 9 GLU HB2 H 2.111 . 2 47 9 9 GLU HB3 H 2.111 . 2 48 9 9 GLU HG2 H 1.814 . 2 49 9 9 GLU HG3 H 1.814 . 2 50 10 10 GLU H H 8.643 . 1 51 10 10 GLU HA H 4.129 . 1 52 10 10 GLU HB2 H 2.012 . 2 53 10 10 GLU HB3 H 1.763 . 2 54 11 11 ALA H H 7.382 . 1 55 11 11 ALA HA H 4.293 . 1 56 11 11 ALA HB H 1.243 . 1 57 12 12 PRO HA H 4.447 . 1 58 12 12 PRO HB2 H 2.254 . 2 59 12 12 PRO HB3 H 1.986 . 2 60 12 12 PRO HD2 H 3.670 . 2 61 12 12 PRO HD3 H 3.670 . 2 62 12 12 PRO HG2 H 1.806 . 2 63 12 12 PRO HG3 H 1.806 . 2 64 13 13 VAL H H 8.549 . 1 65 13 13 VAL HA H 3.674 . 1 66 13 13 VAL HB H 1.986 . 1 67 13 13 VAL HG1 H 0.923 . 2 68 13 13 VAL HG2 H 0.829 . 2 69 14 14 GLU H H 9.063 . 1 70 14 14 GLU HA H 3.896 . 1 71 14 14 GLU HB2 H 1.986 . 2 72 14 14 GLU HB3 H 1.880 . 2 73 14 14 GLU HG2 H 2.293 . 2 74 14 14 GLU HG3 H 2.158 . 2 75 15 15 ASP H H 7.588 . 1 76 15 15 ASP HA H 4.439 . 1 77 15 15 ASP HB2 H 2.689 . 2 78 15 15 ASP HB3 H 2.409 . 2 79 16 16 LEU H H 7.593 . 1 80 16 16 LEU HA H 4.033 . 1 81 16 16 LEU HB2 H 1.553 . 2 82 16 16 LEU HB3 H 1.547 . 2 83 16 16 LEU HD1 H 0.752 . 1 84 16 16 LEU HD2 H 0.752 . 1 85 16 16 LEU HG H 0.752 . 1 86 17 17 ILE H H 8.252 . 1 87 17 17 ILE HA H 3.592 . 1 88 17 17 ILE HB H 1.724 . 1 89 17 17 ILE HD1 H 0.705 . 1 90 17 17 ILE HG12 H 1.579 . 2 91 17 17 ILE HG13 H 0.963 . 2 92 17 17 ILE HG2 H 0.814 . 1 93 18 18 ARG H H 7.499 . 1 94 18 18 ARG HA H 4.002 . 1 95 18 18 ARG HB2 H 1.838 . 2 96 18 18 ARG HB3 H 1.838 . 2 97 18 18 ARG HD2 H 3.149 . 2 98 18 18 ARG HD3 H 3.149 . 2 99 18 18 ARG HE H 6.853 . 1 100 18 18 ARG HG2 H 1.572 . 2 101 18 18 ARG HG3 H 1.721 . 2 102 19 19 PHE H H 7.849 . 1 103 19 19 PHE HA H 4.330 . 1 104 19 19 PHE HB2 H 3.041 . 2 105 19 19 PHE HB3 H 3.166 . 2 106 19 19 PHE HD1 H 6.979 . 1 107 19 19 PHE HD2 H 6.979 . 3 108 19 19 PHE HE1 H 6.979 . 1 109 19 19 PHE HE2 H 6.979 . 3 110 20 20 TYR H H 8.496 . 1 111 20 20 TYR HA H 3.744 . 1 112 20 20 TYR HB2 H 2.876 . 2 113 20 20 TYR HB3 H 3.117 . 2 114 20 20 TYR HD1 H 6.807 . 3 115 20 20 TYR HD2 H 6.807 . 3 116 20 20 TYR HE1 H 6.471 . 3 117 20 20 TYR HE2 H 6.471 . 3 118 21 21 ASN H H 8.174 . 1 119 21 21 ASN HA H 4.231 . 1 120 21 21 ASN HB2 H 2.822 . 2 121 21 21 ASN HB3 H 2.697 . 2 122 21 21 ASN HD21 H 6.455 . 2 123 22 22 ASP H H 8.464 . 1 124 22 22 ASP HA H 4.268 . 1 125 22 22 ASP HB2 H 2.353 . 2 126 22 22 ASP HB3 H 2.353 . 2 127 23 23 LEU H H 8.838 . 1 128 23 23 LEU HA H 3.744 . 1 129 23 23 LEU HB2 H 1.478 . 2 130 23 23 LEU HB3 H 1.329 . 1 131 23 23 LEU HD1 H 0.814 . 2 132 23 23 LEU HD2 H 0.713 . 2 133 23 23 LEU HG H 1.329 . 1 134 24 24 GLN H H 8.114 . 1 135 24 24 GLN HA H 3.478 . 1 136 24 24 GLN HB2 H 2.009 . 2 137 24 24 GLN HB3 H 1.924 . 2 138 24 24 GLN HG2 H 2.135 . 2 139 24 24 GLN HG3 H 2.127 . 2 140 25 25 GLN H H 7.534 . 1 141 25 25 GLN HA H 3.904 . 1 142 25 25 GLN HB2 H 1.981 . 2 143 25 25 GLN HB3 H 1.994 . 2 144 25 25 GLN HG2 H 2.293 . 2 145 25 25 GLN HG3 H 2.283 . 2 146 26 26 TYR H H 7.784 . 1 147 26 26 TYR HA H 4.049 . 1 148 26 26 TYR HB2 H 2.955 . 2 149 26 26 TYR HB3 H 2.923 . 2 150 26 26 TYR HD1 H 6.768 . 3 151 26 26 TYR HD2 H 6.760 . 3 152 26 26 TYR HE1 H 6.424 . 3 153 26 26 TYR HE2 H 6.424 . 3 154 27 27 LEU H H 8.363 . 1 155 27 27 LEU HA H 3.643 . 1 156 27 27 LEU HB2 H 1.643 . 2 157 27 27 LEU HB3 H 1.494 . 2 158 27 27 LEU HD1 H 0.666 . 2 159 27 27 LEU HD2 H 0.478 . 2 160 27 27 LEU HG H 1.119 . 1 161 28 28 ASN H H 7.698 . 1 162 28 28 ASN HA H 4.285 . 1 163 28 28 ASN HB2 H 2.666 . 2 164 28 28 ASN HB3 H 2.662 . 2 165 29 29 VAL H H 7.471 . 1 166 29 29 VAL HA H 3.771 . 1 167 29 29 VAL HB H 1.935 . 1 168 29 29 VAL HG1 H 0.806 . 2 169 29 29 VAL HG2 H 0.679 . 2 170 30 30 VAL H H 7.588 . 1 171 30 30 VAL HA H 3.756 . 1 172 30 30 VAL HB H 1.722 . 1 173 30 30 VAL HG1 H 0.533 . 2 174 30 30 VAL HG2 H 0.494 . 2 stop_ loop_ _Atom_shift_assign_ID_ambiguity 1 34 '2,35' '4,37' '6,39' stop_ save_