data_20015 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR structure of a V3 (SF2 isolate) peptide ; _BMRB_accession_number 20015 _BMRB_flat_file_name bmr20015.str _Entry_type new _Submission_date 2008-04-09 _Accession_date 2008-04-09 _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 Galanakis Petros A. . 2 Kandias Nikolaos G. . 3 Rizos Apostolos . . 4 Morikis Dimitrios . . 5 Krambovitis Elias . . 6 Spyroulias Georgios A. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 73 "13C chemical shifts" 4 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2009-04-03 original author . stop_ save_ ############################# # Citation for this entry # ############################# save_PND_SF2_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'NMR evidence of charge-dependent interaction between various PND V3 and CCR5 N-terminal peptides' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 19117029 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Galanakis Petros A. . 2 Kandias Nikolaos G. . 3 Rizos Apostolos K. . 4 Morikis Dimitrios . . 5 Krambovitis Elias . . 6 Spyroulias Georgios A. . stop_ _Journal_abbreviation Biopolymers _Journal_volume 92 _Journal_issue 2 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 94 _Page_last 109 _Year 2008 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'PND SF2' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'PND SF2' $PND_SF2 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_PND_SF2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common PND_SF2 _Molecular_mass 1481.736 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 13 _Mol_residue_sequence RKSINIGPGRAFY loop_ _Residue_seq_code _Residue_label 1 ARG 2 LYS 3 SER 4 ILE 5 ASN 6 ILE 7 GLY 8 PRO 9 GLY 10 ARG 11 ALA 12 PHE 13 TYR stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $PND_SF2 . . . . . . 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 $PND_SF2 'recombinant technology' . . . . . 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 _Concentration_min_value _Concentration_max_value _Isotopic_labeling $PND_SF2 . mM 2 2.5 'natural abundance' D2O 10 % . . . H2O 90 % . . 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_AMBER _Saveframe_category software _Name AMBER _Version 5.0 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_DYANA _Saveframe_category software _Name DYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Braun and Wuthrich' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_XEASY _Saveframe_category software _Name XEASY _Version . loop_ _Vendor _Address _Electronic_address 'Bartels et al.' . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_xwinnmr _Saveframe_category software _Name xwinnmr _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing stop_ _Details . 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_2D_1H-15N_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H 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 temperature 278 . K pH 7.85 . pH stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7.85 . pH temperature 286 . 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 5.05 internal indirect . . . 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 '2D 1H-1H TOCSY' '2D 1H-1H 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 'PND SF2' _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 1 101 1 ARG HA H 4.071 0.000 . 2 101 1 ARG HB2 H 1.949 0.000 . 3 101 1 ARG HB3 H 1.717 0.000 . 4 101 1 ARG HD2 H 3.243 0.000 . 5 101 1 ARG HD3 H 3.243 0.000 . 6 101 1 ARG HG2 H 1.678 0.000 . 7 101 1 ARG HG3 H 1.678 0.000 . 8 102 2 LYS HA H 4.434 0.000 . 9 102 2 LYS HB2 H 1.878 0.000 . 10 102 2 LYS HB3 H 1.825 0.000 . 11 102 2 LYS HD2 H 1.778 0.000 . 12 102 2 LYS HD3 H 1.778 0.000 . 13 102 2 LYS HE2 H 3.113 0.000 . 14 102 2 LYS HE3 H 3.113 0.000 . 15 102 2 LYS HG2 H 1.513 0.000 . 16 102 2 LYS HG3 H 1.513 0.000 . 17 103 3 SER H H 8.705 0.000 . 18 103 3 SER HA H 4.520 0.000 . 19 103 3 SER HB2 H 3.865 0.000 . 20 103 3 SER HB3 H 3.865 0.000 . 21 104 4 ILE H H 8.360 0.000 . 22 104 4 ILE HA H 4.235 0.000 . 23 104 4 ILE HB H 1.854 0.000 . 24 104 4 ILE HD1 H 0.862 0.000 . 25 104 4 ILE HG12 H 1.347 0.000 . 26 104 4 ILE HG13 H 1.152 0.000 . 27 104 4 ILE HG2 H 0.889 0.000 . 28 105 5 ASN H H 8.549 0.000 . 29 105 5 ASN HA H 4.591 0.000 . 30 105 5 ASN HB2 H 2.987 0.000 . 31 105 5 ASN HB3 H 2.934 0.000 . 32 105 5 ASN HD21 H 7.106 0.000 . 33 105 5 ASN HD22 H 6.793 0.000 . 34 106 6 ILE H H 8.148 0.000 . 35 106 6 ILE HA H 4.167 0.000 . 36 106 6 ILE HB H 1.798 0.000 . 37 106 6 ILE HD1 H 0.837 0.000 . 38 106 6 ILE HG12 H 1.417 0.000 . 39 106 6 ILE HG13 H 1.115 0.000 . 40 106 6 ILE HG2 H 0.875 0.000 . 41 107 7 GLY H H 7.742 0.000 . 42 107 7 GLY HA2 H 4.018 0.000 . 43 107 7 GLY HA3 H 4.018 0.000 . 44 108 8 PRO HA H 4.513 0.000 . 45 108 8 PRO HB2 H 2.325 0.000 . 46 108 8 PRO HB3 H 2.085 0.000 . 47 108 8 PRO HD2 H 3.715 0.000 . 48 108 8 PRO HD3 H 3.672 0.000 . 49 108 8 PRO HG2 H 2.044 0.000 . 50 108 8 PRO HG3 H 2.044 0.000 . 51 109 9 GLY H H 8.716 0.000 . 52 109 9 GLY HA2 H 3.981 0.000 . 53 109 9 GLY HA3 H 3.981 0.000 . 54 110 10 ARG H H 8.200 0.001 . 55 110 10 ARG HA H 4.295 0.000 . 56 110 10 ARG HB2 H 1.770 0.000 . 57 110 10 ARG HB3 H 1.669 0.000 . 58 110 10 ARG HD2 H 3.103 0.000 . 59 110 10 ARG HD3 H 3.103 0.000 . 60 110 10 ARG HG2 H 1.522 0.000 . 61 110 10 ARG HG3 H 1.522 0.000 . 62 111 11 ALA H H 8.397 0.000 . 63 111 11 ALA HA H 4.244 0.001 . 64 111 11 ALA HB H 1.269 0.000 . 65 112 12 PHE H H 8.170 0.000 . 66 112 12 PHE HA H 4.586 0.001 . 67 112 12 PHE HB2 H 3.126 0.000 . 68 112 12 PHE HB3 H 2.954 0.000 . 69 112 12 PHE HZ H 7.309 0.000 . 70 112 12 PHE CG C 7.229 0.000 . 71 112 12 PHE CZ C 7.351 0.000 . 72 113 13 TYR H H 7.775 0.000 . 73 113 13 TYR HA H 4.373 0.000 . 74 113 13 TYR HB2 H 3.089 0.000 . 75 113 13 TYR HB3 H 2.890 0.000 . 76 113 13 TYR CG C 7.113 0.000 . 77 113 13 TYR CZ C 6.839 0.000 . stop_ save_ save_constraint_statistics _Saveframe_category constraint_statistics _Text_data_format . _Text_data . _NOE_interproton_distance_evaluation . _NOE_pseudoatom_corrections . _Details . save_