data_5542 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; 1H chemical shifts for Penetratin in phospolipid bicelles ; _BMRB_accession_number 5542 _BMRB_flat_file_name bmr5542.str _Entry_type original _Submission_date 2002-10-01 _Accession_date 2002-10-01 _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 Lindberg Mattias . . 2 Biverstahl Henrik . . 3 Graslund Astrid . . 4 Maler Lena . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 66 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-10-30 update BMRB 'update entry etc.' 2003-08-01 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 5543 'Penetratin(W48F,W56F) in phospolipid bicelles and SDS micelles.' stop_ _Original_release_date 2002-10-01 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structure and Positioning Comparison of Two Variants of Penetratin in Two Different Membrane Mimicking Systems by NMR ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 22731168 _PubMed_ID 12846839 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Lindberg Mattias . . 2 Biverstahl Henrik . . 3 Graslund Astrid . . 4 Maler Lena . . stop_ _Journal_abbreviation 'Eur. J. Biochem.' _Journal_volume 270 _Journal_issue 14 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 3055 _Page_last 3063 _Year 2003 _Details . save_ ################################## # Molecular system description # ################################## save_system_Penetratin _Saveframe_category molecular_system _Mol_system_name Penetratin _Abbreviation_common Penetratin _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label Penetratin $Penetratin stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_Penetratin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common Penetratin _Abbreviation_common Penetratin _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 16 _Mol_residue_sequence ; RQIKIWFQNRRMKWKK ; loop_ _Residue_seq_code _Residue_label 1 ARG 2 GLN 3 ILE 4 LYS 5 ILE 6 TRP 7 PHE 8 GLN 9 ASN 10 ARG 11 ARG 12 MET 13 LYS 14 TRP 15 LYS 16 LYS stop_ _Sequence_homology_query_date 2008-08-19 _Sequence_homology_query_revised_last_date 2008-08-19 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 DBJ BAA01947 'Hox 3.5 [Mus musculus]' 100.00 264 100.00 100.00 1.49e-02 DBJ BAA76868 'Scr [Bombyx mori]' 100.00 356 100.00 100.00 9.40e-03 DBJ BAA78622 'AmphiHox4 [Branchiostoma floridae]' 100.00 275 100.00 100.00 9.40e-03 DBJ BAA86238 'HOXC4A [Oryzias latipes]' 100.00 261 100.00 100.00 1.97e-02 DBJ BAB28059 'unnamed protein product [Mus musculus]' 100.00 230 100.00 100.00 2.20e-02 EMBL CAA07498 'homeobox protein [Cupiennius salei]' 100.00 263 100.00 100.00 1.89e-02 EMBL CAA28411 'unnamed protein product [Homo sapiens]' 100.00 255 100.00 100.00 9.40e-03 EMBL CAA28782 'unnamed protein product [Drosophila melanogaster]' 100.00 590 100.00 100.00 9.40e-03 EMBL CAA29934 'unnamed protein product [Mus musculus]' 100.00 217 100.00 100.00 3.10e-02 EMBL CAA30125 'unnamed protein product [Xenopus laevis]' 100.00 230 100.00 100.00 2.06e-02 GenBank AAA20072 'homeobox protein' 100.00 248 100.00 100.00 9.40e-03 GenBank AAA28375 'deformed protein' 100.00 427 100.00 100.00 9.88e-03 GenBank AAA36003 'homeobox c1 protein' 100.00 217 100.00 100.00 1.54e-02 GenBank AAA37833 'hox-1.1 peptide' 100.00 229 100.00 100.00 1.23e-02 GenBank AAA37837 'homeo domain protein' 100.00 270 100.00 100.00 9.40e-03 PRF 1301323A 'gene homeobox' 100.00 255 100.00 100.00 9.40e-03 PRF 1305251A 'Deformed gene' 100.00 590 100.00 100.00 9.40e-03 PRF 1916397A 'Hox3.5 gene' 100.00 264 100.00 100.00 1.49e-02 REF NP_001011405 'homeobox A5 [Xenopus tropicalis]' 100.00 274 100.00 100.00 1.13e-02 REF NP_001017480 'homeo box B7 [Rattus norvegicus]' 100.00 219 100.00 100.00 3.31e-02 REF NP_001020526 'homeo box B5 [Gallus gallus]' 100.00 264 100.00 100.00 9.88e-03 REF NP_001034510 'transcription factor deformed [Tribolium castaneum]' 100.00 412 100.00 100.00 9.40e-03 REF NP_001034523 'cephalothorax [Tribolium castaneum]' 100.00 312 100.00 100.00 9.40e-03 SWISS-PROT A1YER7 'Homeobox protein Hox-D4' 100.00 255 100.00 100.00 9.40e-03 SWISS-PROT A1YFA5 'Homeobox protein Hox-B7' 100.00 217 100.00 100.00 5.60e-02 SWISS-PROT A1YFD8 'Homeobox protein Hox-D4' 100.00 255 100.00 100.00 9.40e-03 SWISS-PROT A1YFY3 'Homeobox protein Hox-D4' 100.00 255 100.00 100.00 9.40e-03 SWISS-PROT A2D4P8 'Homeobox protein Hox-D4' 100.00 255 100.00 100.00 9.40e-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 _Details $Penetratin . . . . . . Unclassified. 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 $Penetratin 'cell free synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type bicell_solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Penetratin 2 mM . DMPC 10 mM . DMPG 90 mM . DHPC 192 mM . stop_ save_ ############################ # Computer software used # ############################ save_VNMR _Saveframe_category software _Name VNMR _Version . _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model Unity _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _Sample_label . save_ save_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _Sample_label . save_ ####################### # Sample conditions # ####################### save_Conditions _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 5.5 0.1 n/a temperature 318 1 K 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 TSP H 1 'methyl protons' ppm 0.00 internal direct spherical internal parallel 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_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label NOESY TOCSY stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $Conditions _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name Penetratin _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 . 2 GLN H H 8.52 0.01 1 2 . 2 GLN HA H 4.48 0.01 1 3 . 2 GLN HB2 H 2.07 0.01 2 4 . 2 GLN HB3 H 2.15 0.01 2 5 . 2 GLN HG2 H 2.42 0.01 1 6 . 2 GLN HG3 H 2.42 0.01 1 7 . 3 ILE H H 8.57 0.01 1 8 . 3 ILE HA H 4.13 0.01 1 9 . 3 ILE HB H 1.95 0.01 1 10 . 3 ILE HG12 H 1.24 0.01 2 11 . 3 ILE HG2 H 0.96 0.01 1 12 . 3 ILE HD1 H 0.90 0.01 1 13 . 4 LYS H H 8.39 0.01 1 14 . 4 LYS HA H 4.27 0.01 1 15 . 4 LYS HG2 H 1.39 0.01 4 16 . 5 ILE H H 7.79 0.01 1 17 . 5 ILE HA H 4.09 0.01 1 18 . 5 ILE HB H 1.88 0.01 1 19 . 5 ILE HG12 H 1.21 0.01 2 20 . 5 ILE HG2 H 0.85 0.01 4 21 . 5 ILE HD1 H 0.85 0.01 4 22 . 6 TRP H H 8.03 0.01 1 23 . 6 TRP HA H 4.40 0.01 1 24 . 6 TRP HB2 H 3.30 0.01 2 25 . 6 TRP HB3 H 3.26 0.01 2 26 . 6 TRP HD1 H 7.45 0.01 4 27 . 7 PHE H H 8.01 0.01 1 28 . 7 PHE HA H 4.09 0.01 1 29 . 7 PHE HB2 H 3.15 0.01 1 30 . 7 PHE HB3 H 3.15 0.01 1 31 . 8 GLN H H 8.27 0.01 1 32 . 8 GLN HA H 4.14 0.01 1 33 . 8 GLN HB2 H 2.11 0.01 2 34 . 8 GLN HG2 H 2.40 0.01 2 35 . 8 GLN HG3 H 2.44 0.01 2 36 . 9 ASN H H 8.40 0.01 1 37 . 9 ASN HA H 4.59 0.01 1 38 . 9 ASN HB2 H 2.75 0.01 2 39 . 9 ASN HB3 H 2.83 0.01 2 40 . 10 ARG H H 8.00 0.01 1 41 . 10 ARG HA H 4.23 0.01 1 42 . 10 ARG HB2 H 1.73 0.01 2 43 . 10 ARG HB3 H 1.83 0.01 2 44 . 11 ARG H H 8.10 0.01 1 45 . 11 ARG HA H 4.13 0.01 1 46 . 11 ARG HB2 H 1.77 0.01 2 47 . 11 ARG HB3 H 1.84 0.01 2 48 . 12 MET H H 8.05 0.01 1 49 . 12 MET HA H 4.30 0.01 1 50 . 12 MET HB2 H 1.98 0.01 2 51 . 12 MET HG2 H 2.50 0.01 2 52 . 12 MET HG3 H 2.53 0.01 2 53 . 13 LYS H H 7.97 0.01 1 54 . 13 LYS HA H 4.24 0.01 1 55 . 13 LYS HB2 H 1.63 0.01 2 56 . 13 LYS HB3 H 1.73 0.01 2 57 . 13 LYS HG2 H 1.36 0.01 4 58 . 14 TRP H H 7.98 0.01 1 59 . 14 TRP HA H 4.71 0.01 1 60 . 14 TRP HB2 H 3.22 0.01 2 61 . 14 TRP HB3 H 3.33 0.01 2 62 . 14 TRP HD1 H 7.47 0.01 4 63 . 15 LYS H H 8.11 0.01 1 64 . 15 LYS HA H 4.20 0.01 1 65 . 15 LYS HG2 H 1.45 0.01 4 66 . 15 LYS HG3 H 1.50 0.01 4 stop_ loop_ _Atom_shift_assign_ID_ambiguity 15 '20,21' 26 57 62 '65,66' stop_ save_