data_18184 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; ShB peptide structure bound to negatively charged lipid-bilayer after Molecular Dynamics refinement ; _BMRB_accession_number 18184 _BMRB_flat_file_name bmr18184.str _Entry_type original _Submission_date 2012-01-06 _Accession_date 2012-01-06 _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 Weingarth Markus . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "13C chemical shifts" 43 "15N chemical shifts" 11 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-02-12 update BMRB 'update entry citation' 2012-08-06 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Supramolecular structure of membrane-associated polypeptides by combining solid-state NMR and molecular dynamics simulations.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 22828329 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Weingarth Markus . . 2 Ader Christian . . 3 Melquiond Adrien S.J. . 4 Nand Deepak . . 5 Pongs Olaf . . 6 Becker Stefan . . 7 Bonvin 'Alexandre M J J' . . 8 Baldus Marc . . stop_ _Journal_abbreviation 'Biophys. J.' _Journal_name_full 'Biophysical journal' _Journal_volume 103 _Journal_issue 1 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 29 _Page_last 37 _Year 2012 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'ShB peptide' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'ShB peptide' $entity 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_entity _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity _Molecular_mass 2233.591 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 20 _Mol_residue_sequence MAAVAGLYGLGEDRQHRKKQ loop_ _Residue_seq_code _Residue_label 1 MET 2 ALA 3 ALA 4 VAL 5 ALA 6 GLY 7 LEU 8 TYR 9 GLY 10 LEU 11 GLY 12 GLU 13 ASP 14 ARG 15 GLN 16 HIS 17 ARG 18 LYS 19 LYS 20 GLN stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-11-04 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 2LNY "Shb Peptide Structure Bound To Negatively Charged Lipid-Bilayer After Molecular Dynamics Refinement" 100.00 20 100.00 100.00 5.05e-04 EMBL CAA29917 "Shaker [Drosophila melanogaster]" 100.00 656 100.00 100.00 1.25e-03 EMBL CAA30143 "unnamed protein product [Drosophila melanogaster]" 100.00 616 100.00 100.00 5.78e-04 EMBL CAA30146 "unnamed protein product [Drosophila melanogaster]" 100.00 349 100.00 100.00 2.45e-04 GB AAA28417 "potassium channel component [Drosophila melanogaster]" 100.00 616 100.00 100.00 5.78e-04 GB AAF48785 "shaker, isoform B [Drosophila melanogaster]" 100.00 616 100.00 100.00 5.25e-04 GB AAF48786 "shaker, isoform E [Drosophila melanogaster]" 100.00 655 100.00 100.00 1.21e-03 GB AAS65396 "shaker, isoform F [Drosophila melanogaster]" 100.00 349 100.00 100.00 2.45e-04 GB AGB95507 "shaker, isoform Q [Drosophila melanogaster]" 100.00 616 100.00 100.00 5.25e-04 PRF 1402312A "K channel protein" 100.00 656 100.00 100.00 1.25e-03 REF NP_001259665 "shaker, isoform Q [Drosophila melanogaster]" 100.00 616 100.00 100.00 5.25e-04 REF NP_001303569 "shaker, isoform T [Drosophila melanogaster]" 100.00 655 100.00 100.00 1.40e-03 REF NP_523393 "shaker, isoform B [Drosophila melanogaster]" 100.00 616 100.00 100.00 5.25e-04 REF NP_728123 "shaker, isoform E [Drosophila melanogaster]" 100.00 655 100.00 100.00 1.21e-03 REF NP_996497 "shaker, isoform F [Drosophila melanogaster]" 100.00 349 100.00 100.00 2.45e-04 SP P08510 "RecName: Full=Potassium voltage-gated channel protein Shaker; AltName: Full=Protein minisleep" 100.00 655 100.00 100.00 1.21e-03 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity . . . . . . 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 $entity 'obtained from a collaborator' . Escherichia coli . . 'coding sequewnce of ShB peptide was cloned into a modified pMal vector (NEB)' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solid _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling DOPC 7 mM 'natural abundance' Cardiolipin 3 mM 'natural abundance' H2O 100 % 'natural abundance' 'sodium citrate' 100 mM 'natural abundance' Calbiochem 4 mM 'natural abundance' $entity 0.055 mg/uL 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_GROMOS _Saveframe_category software _Name GROMOS _Version 53a6 loop_ _Vendor _Address _Electronic_address 'van Gunsteren and Berendsen' . . stop_ loop_ _Task refinement stop_ _Details 'with the Berger lipid parameter' save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 500 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 700 _Details . save_ ############################# # NMR applied experiments # ############################# save_13C-13C_PARISxy_1 _Saveframe_category NMR_applied_experiment _Experiment_name '13C-13C PARISxy' _Sample_label $sample_1 save_ save_13c-13C_PDSD_2 _Saveframe_category NMR_applied_experiment _Experiment_name '13c-13C PDSD' _Sample_label $sample_1 save_ save_SPECIFIC-NCA_3 _Saveframe_category NMR_applied_experiment _Experiment_name SPECIFIC-NCA _Sample_label $sample_1 save_ save_SPECIFIC-NCO_4 _Saveframe_category NMR_applied_experiment _Experiment_name SPECIFIC-NCO _Sample_label $sample_1 save_ save_CHHC_5 _Saveframe_category NMR_applied_experiment _Experiment_name CHHC _Sample_label $sample_1 save_ save_NHHC_6 _Saveframe_category NMR_applied_experiment _Experiment_name NHHC _Sample_label $sample_1 save_ save_HHC_7 _Saveframe_category NMR_applied_experiment _Experiment_name HHC _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 temperature 280 3 K pH 4.0 . pH 'ionic strength' 0.3 . M 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 Adamantane C 13 'methyl carbon' ppm 31.48 external direct . . . 1 AGG N 15 nitrogen ppm 38.9 external 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 _Details . loop_ _Experiment_label '13C-13C PARISxy' '13c-13C PDSD' SPECIFIC-NCA SPECIFIC-NCO 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 'ShB peptide' _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 CA C 54.8 . . 2 1 1 MET CB C 32.3 . . 3 1 1 MET CG C 30.7 . . 4 1 1 MET CE C 17.2 . . 5 2 2 ALA C C 175.4 . . 6 2 2 ALA CA C 51.2 . . 7 2 2 ALA CB C 23.5 . . 8 2 2 ALA N N 123.4 . . 9 3 3 ALA C C 175.4 . . 10 3 3 ALA CA C 51.1 . . 11 3 3 ALA CB C 23.6 . . 12 3 3 ALA N N 120.7 . . 13 4 4 VAL C C 172.6 . . 14 4 4 VAL CA C 59.5 . . 15 4 4 VAL CB C 35.9 . . 16 4 4 VAL N N 115.8 . . 17 4 4 VAL CG1 C 21.2 . . 18 5 5 ALA C C 176.0 . . 19 5 5 ALA CA C 51.2 . . 20 5 5 ALA CB C 23.6 . . 21 5 5 ALA N N 124.1 . . 22 6 6 GLY C C 169.7 . . 23 6 6 GLY CA C 47.2 . . 24 6 6 GLY N N 106.4 . . 25 7 7 LEU C C 173.4 . . 26 7 7 LEU CA C 52.9 . . 27 7 7 LEU CB C 46.8 . . 28 7 7 LEU CD1 C 23.2 . . 29 7 7 LEU CD2 C 23.2 . . 30 7 7 LEU CG C 26.8 . . 31 7 7 LEU N N 116.1 . . 32 8 8 TYR C C 175.2 . . 33 8 8 TYR CA C 55.7 . . 34 8 8 TYR CB C 46.8 . . 35 8 8 TYR N N 116.2 . . 36 9 9 GLY C C 170.5 . . 37 9 9 GLY CA C 46.0 . . 38 9 9 GLY N N 104.5 . . 39 10 10 LEU C C 175.3 . . 40 10 10 LEU CA C 54.7 . . 41 10 10 LEU CB C 45.7 . . 42 10 10 LEU CD1 C 23.7 . . 43 10 10 LEU CD2 C 23.7 . . 44 10 10 LEU N N 119.5 . . 45 10 10 LEU CG C 26.6 . . 46 11 11 GLY C C 170.6 . . 47 11 11 GLY CA C 46.1 . . 48 11 11 GLY N N 104.9 . . 49 12 12 GLU C C 171.7 . . 50 12 12 GLU CA C 54.6 . . 51 12 12 GLU CB C 29.8 . . 52 12 12 GLU CG C 34.0 . . 53 12 12 GLU CD C 180.0 . . 54 12 12 GLU N N 122.4 . . stop_ save_