data_20019 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR structure of a V3 (MN isolate) peptide ; _BMRB_accession_number 20019 _BMRB_flat_file_name bmr20019.str _Entry_type original _Submission_date 2008-04-10 _Accession_date 2008-04-10 _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" 86 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-06-03 update BMRB 'edit entity name' 2009-04-03 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_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 94 _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 MN' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'PND MN' $entity PND $PND 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 'PND MN' _Molecular_mass 1418.734 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 13 _Mol_residue_sequence RKRIHIGPGRAFY loop_ _Residue_seq_code _Residue_label 1 ARG 2 LYS 3 ARG 4 ILE 5 HIS 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_ ############# # Ligands # ############# save_PND _Saveframe_category ligand _Mol_type non-polymer _Name_common "PND (P-NITROPHENYLHYDRAZINE)" _BMRB_code . _PDB_code PND _Molecular_mass 153.139 _Mol_charge 0 _Mol_paramagnetic . _Mol_aromatic yes _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Fri Feb 15 20:30:47 2008 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N1 N1 N N 0 . ? C1 C1 C N 0 . ? N2 N2 N N 0 . ? C2 C2 C N 0 . ? C3 C3 C N 0 . ? C4 C4 C N 0 . ? N4 N4 N N 1 . ? O3 O3 O N -1 . ? O4 O4 O N 0 . ? C5 C5 C N 0 . ? C6 C6 C N 0 . ? HN11 HN11 H N 0 . ? HN12 HN12 H N 0 . ? HN2 HN2 H N 0 . ? H2 H2 H N 0 . ? H3 H3 H N 0 . ? H5 H5 H N 0 . ? H6 H6 H N 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 N1 N2 ? ? SING N1 HN11 ? ? SING N1 HN12 ? ? SING C1 N2 ? ? DOUB C1 C2 ? ? SING C1 C6 ? ? SING N2 HN2 ? ? SING C2 C3 ? ? SING C2 H2 ? ? DOUB C3 C4 ? ? SING C3 H3 ? ? SING C4 N4 ? ? SING C4 C5 ? ? SING N4 O3 ? ? DOUB N4 O4 ? ? DOUB C5 C6 ? ? SING C5 H5 ? ? SING C6 H6 ? ? stop_ _Mol_thiol_state . _Sequence_homology_query_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Details $entity . . . . . . 'HUMAN IMMUNODEFICIENCY VIRUS TYPE 1' 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 $entity '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 $entity . mM 2 2.5 'natural abundance' $PND . 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_ _Software_label $XEASY stop_ 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 MN' _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 ARG HA H 4.042 0.003 1 2 1 1 ARG HB2 H 1.934 0.003 2 3 1 1 ARG HB3 H 1.700 0.001 2 4 1 1 ARG HD2 H 3.240 0.003 1 5 1 1 ARG HD3 H 3.240 0.003 1 6 1 1 ARG HG2 H 1.665 0.001 1 7 1 1 ARG HG3 H 1.665 0.001 1 8 2 2 LYS HA H 4.387 0.003 1 9 2 2 LYS HB2 H 1.831 0.004 2 10 2 2 LYS HB3 H 1.723 0.003 2 11 2 2 LYS HD2 H 1.512 0.003 1 12 2 2 LYS HD3 H 1.512 0.003 1 13 2 2 LYS HE2 H 3.031 0.002 1 14 2 2 LYS HE3 H 3.031 0.002 1 15 2 2 LYS HG2 H 1.459 0.003 1 16 2 2 LYS HG3 H 1.459 0.003 1 17 3 3 ARG H H 8.716 0.003 1 18 3 3 ARG HA H 4.374 0.001 1 19 3 3 ARG HB2 H 1.786 0.001 2 20 3 3 ARG HB3 H 1.653 0.001 2 21 3 3 ARG HD2 H 3.184 0.003 1 22 3 3 ARG HD3 H 3.184 0.003 1 23 3 3 ARG HE H 7.306 0.001 1 24 3 3 ARG HG2 H 1.572 0.002 1 25 3 3 ARG HG3 H 1.572 0.002 1 26 4 4 ILE H H 8.434 0.003 1 27 4 4 ILE HA H 4.198 0.003 1 28 4 4 ILE HB H 1.831 0.003 1 29 4 4 ILE HD1 H 0.877 0.003 1 30 4 4 ILE HG12 H 1.459 0.003 1 31 4 4 ILE HG13 H 1.459 0.003 1 32 4 4 ILE HG2 H 1.190 0.003 1 33 5 5 HIS H H 8.694 0.001 1 34 5 5 HIS HA H 4.702 0.003 1 35 5 5 HIS HB2 H 3.113 0.001 2 36 5 5 HIS HB3 H 3.048 0.003 2 37 5 5 HIS HD2 H 7.034 0.001 1 38 5 5 HIS HE1 H 7.977 0.003 1 39 6 6 ILE H H 8.309 0.003 1 40 6 6 ILE HA H 4.231 0.003 1 41 6 6 ILE HB H 1.843 0.003 1 42 6 6 ILE HD1 H 0.860 0.003 1 43 6 6 ILE HG12 H 1.456 0.002 1 44 6 6 ILE HG13 H 1.456 0.002 1 45 6 6 ILE HG2 H 0.917 0.001 1 46 7 7 GLY H H 8.422 0.002 1 47 7 7 GLY HA2 H 4.136 0.003 1 48 7 7 GLY HA3 H 4.136 0.003 1 49 8 8 PRO HA H 4.506 0.003 1 50 8 8 PRO HB2 H 2.319 0.001 2 51 8 8 PRO HB3 H 2.069 0.001 2 52 8 8 PRO HD2 H 3.711 0.003 2 53 8 8 PRO HD3 H 3.667 0.003 2 54 8 8 PRO HG2 H 2.029 0.003 1 55 8 8 PRO HG3 H 2.029 0.003 1 56 9 9 GLY H H 8.714 0.003 1 57 9 9 GLY HA2 H 3.974 0.001 1 58 9 9 GLY HA3 H 3.974 0.001 1 59 10 10 ARG H H 8.212 0.001 1 60 10 10 ARG HA H 4.260 0.003 1 61 10 10 ARG HB2 H 1.779 0.003 2 62 10 10 ARG HB3 H 1.683 0.003 2 63 10 10 ARG HD2 H 3.128 0.003 1 64 10 10 ARG HD3 H 3.128 0.003 1 65 10 10 ARG HE H 7.225 0.002 1 66 10 10 ARG HG2 H 1.533 0.003 1 67 10 10 ARG HG3 H 1.533 0.003 1 68 11 11 ALA H H 8.384 0.001 1 69 11 11 ALA HA H 4.260 0.005 1 70 11 11 ALA HB H 1.268 0.002 1 71 12 12 PHE H H 8.194 0.001 1 72 12 12 PHE HA H 4.618 0.002 1 73 12 12 PHE HB2 H 3.127 0.003 2 74 12 12 PHE HB3 H 2.946 0.003 2 75 12 12 PHE HD1 H 7.223 0.003 1 76 12 12 PHE HD2 H 7.223 0.003 1 77 12 12 PHE HE1 H 7.342 0.003 1 78 12 12 PHE HE2 H 7.342 0.003 1 79 13 13 TYR H H 7.815 0.003 1 80 13 13 TYR HA H 4.371 0.003 1 81 13 13 TYR HB2 H 3.099 0.003 2 82 13 13 TYR HB3 H 2.896 0.003 2 83 13 13 TYR HD1 H 7.105 0.003 1 84 13 13 TYR HD2 H 7.105 0.003 1 85 13 13 TYR HE1 H 6.821 0.002 1 86 13 13 TYR HE2 H 6.821 0.002 1 stop_ save_