data_7006 #Corrected using PDB structure: 2DEZA # #N.B. (Observed* = Observed shift + Offset correction) # #After reference correction, the following residues still #have a HA chemical shift difference (obs*-pred) greater than 0.7ppm: #NUM AA CS Observed* Predicted # 4 K HA 3.52 4.52 # 21 Y HA 3.98 3.21 # #The average CS difference between predicted and observed: #HA CA CB CO N HN #-0.02 N/A N/A N/A N/A 0.03 # #bmr7006.str.corr chemical shifts have been re-referenced with the following #offsets (these values have been added to the original bmr7006.str file): #HA CA CB CO N HN #N/A N/A N/A N/A N/A N/A # #The 95% confidence intervals for the above recommended offsets are: # HA CA CB CO N HN #+/-0.05 N/A N/A N/A N/A +/-0.11 # #The Correlation Coefficients between predicted and observed #chemical shifts are: #HA CA CB CO N HN #0.382 N/A N/A N/A N/A -0.013 # #The RMSD between predicted and observed* (reference #corrected) chemical shifts are: #HA CA CB CO N HN #0.148 N/A N/A N/A N/A 0.292 # ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of human PYY ; loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Nygaard R. . . stop_ _BMRB_accession_number 7006 _BMRB_flat_file_name bmr7006.str _Entry_type new _Submission_date 2006-02-28 _Accession_date 2006-02-28 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count '1H chemical shifts' 175 stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_title ; The PP-Fold Solution Structure of Human Polypeptide YY and Human PYY3-36 As Determined by NMR(,). ; _Citation_status published _Citation_type journal _MEDLINE_UI_code . _PubMed_ID 16819834 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Nygaard R. . . 2 Nielbo S. . . 3 Schwartz T. W. . 4 Poulsen F. M. . stop_ _Journal_abbreviation Biochemistry _Journal_volume 45 _Journal_issue 27 _Page_first 8350 _Page_last 8357 _Year 2006 loop_ _Keyword "PP-fold" "helix" "peptide" "neuropeptide" stop_ save_ ################################## # Molecular system description # ################################## save_system _Saveframe_category molecular_system _Mol_system_name "Peptide YY" _Abbreviation_common "Peptide YY" _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label "Peptide YY" $YY stop_ _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'not present' loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Database_entry_details PDB 2DEZ ? . stop_ save_ ######################## # Monomeric polymers # ######################## save_YY _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common "Peptide YY" _Name_variant . _Abbreviation_common "Peptide YY" _Mol_thiol_state 'not present' ############################## # Polymer residue sequence # ############################## _Residue_count 36 _Mol_residue_sequence ; YPIKPEAPGEDASPEELNRY YASLRHYLNLVTRQRX ; loop_ _Residue_seq_code _Residue_label 1 TYR 2 PRO 3 ILE 4 LYS 5 PRO 6 GLU 7 ALA 8 PRO 9 GLY 10 GLU 11 ASP 12 ALA 13 SER 14 PRO 15 GLU 16 GLU 17 LEU 18 ASN 19 ARG 20 TYR 21 TYR 22 ALA 23 SER 24 LEU 25 ARG 26 HIS 27 TYR 28 LEU 29 ASN 30 LEU 31 VAL 32 THR 33 ARG 34 GLN 35 ARG 36 TYR_NH2 stop_ _Sequence_homology_query_date 2006-10-26 _Sequence_homology_query_revised_last_date 2006-10-26 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 BMRB 7005 "Peptide YY" 105.88 34 100 100 10e-12 PDB 2DF0 "A Chain A, Solution Structure Of HumanPyy3-36" 102.86 35 100 100 10e-12 PDB 2DEZ "A Chain A, Structure Of Human Pyy" 97.30 37 100 100 3e-13 DBJ BAA02998.1 "peptide YY precursor variant [Homosapiens]" 40.00 90 100 100 3e-13 DBJ BAA03002.1 "peptide YY precursor [Homo sapiens]" 40.00 90 100 100 3e-13 DBJ BAA02997.1 "peptide YY precursor [Homo sapiens]" 37.11 97 100 100 3e-13 DBJ BAA03000.1 "peptide YY precursor [Homo sapiens]" 37.11 97 100 100 3e-13 EMBL CAG46926.1 "PYY [Homo sapiens]" 40.00 90 100 100 3e-13 GenBank AAB32642.1 "peptide YY, PYY(3-36) [rabbits,intestinal mucosa, Peptide, 34 aa]" 105.88 34 100 100 3e-11 GenBank AAA36433.1 "peptide YY [Homo sapiens]" 37.11 97 100 100 3e-13 GenBank AAH41057.1 "Peptide YY [Homo sapiens]" 37.11 97 100 100 3e-13 PIR A31358 "peptide YY - human" 100.00 36 100 100 3e-13 PIR S34568 "peptide YY precursor (clone L1) - human(fragment)" 40.00 90 100 100 3e-13 REF XP_523780.2 "PREDICTED: peptide YY [Pantroglodytes]" 35.64 101 100 100 3e-13 SWISS-PROT P10082 "PYY_HUMAN Peptide YY precursor (PYY) (PYY-I)(Peptide tyrosine tyrosine) [Contains: Peptide YY(3-36)(PYY-II)]" 37.11 97 100 100 3e-13 stop_ save_ ###################### # Polymer residues # ###################### save_TYR_NH2 _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common 'L-TYROSINAMIDE' _Abbreviation_common TYR-NH2 _Name_IUPAC . _BMRB_code TYR_NH2 _PDB_code . _Standard_residue_derivative TYR loop_ _Mol_label _Residue_seq_code $YY 36 stop_ _Mol_empirical_formula 'C9 H11 N2 O2' _Mol_paramagnetic no _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N ? 0 ? ? NT NT N ? 0 ? ? CA CA C ? 0 ? ? C C C ? 0 ? ? O O O ? 0 ? ? CB CB C ? 0 ? ? CG CG C ? 0 ? ? CD1 CD1 C ? 0 ? ? CD2 CD2 C ? 0 ? ? CE1 CE1 C ? 0 ? ? CE2 CE2 C ? 0 ? ? CZ CZ C ? 0 ? ? OH OH O ? 0 ? ? H H H ? 0 ? ? HA HA H ? 0 ? ? HB2 1HB H ? 0 ? ? HB3 2HB H ? 0 ? ? HD1 HD1 H ? 0 ? ? HD2 HD2 H ? 0 ? ? HE1 HE1 H ? 0 ? ? HE2 HE2 H ? 0 ? ? HH HH H ? 0 ? ? HT1 1HNT H ? 0 ? ? HT2 2HNT H ? 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 N CA N CA SING N H N H SING CA C CA C SING CA CB CA CB SING CA HA CA HA DOUB C O C O SING CB CG CB CG SING CB HB2 CB 1HB SING CB HB3 CB 2HB DOUB CG CD1 CG CD1 SING CG CD2 CG CD2 SING CD1 CE1 CD1 CE1 SING CD1 HD1 CD1 HD1 DOUB CD2 CE2 CD2 CE2 SING CD2 HD2 CD2 HD2 DOUB CE1 CZ CE1 CZ SING CE1 HE1 CE1 HE1 SING CE2 CZ CE2 CZ SING CE2 HE2 CE2 HE2 SING CZ OH CZ OH SING OH HH OH HH SING NT C NT C SING NT HT1 NT 1HNT SING NT HT2 NT 2HNT stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $YY Human 9606 Eukaryota Metazoa Homo sapiens 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 $YY "recombinant technology" . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $YY 1 mM . NaOH ? ? ? HCl ? ? ? H2O 90 % ? D2O 10 % ? stop_ save_ ############################ # Computer software used # ############################ save_NMRPipe _Saveframe_category software _Name NMRPipe loop_ _Task processing stop_ _Details "Delaglio, F." save_ save_Pronto3D _Saveframe_category software _Name Pronto3D loop_ _Task "data analysis" stop_ _Details "Kjaer, M." save_ save_CYANA _Saveframe_category software _Name CYANA _Version 1.0 loop_ _Task "structure solution" stop_ _Details "Guntert, P." save_ save_XPLOR-NIH _Saveframe_category software _Name XPLOR-NIH _Version 2.9 loop_ _Task "structure solution" stop_ _Details "Schwieters, C." save_ save_CNS _Saveframe_category software _Name CNS _Version 1.1 loop_ _Task refinement stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 750 save_ ############################# # NMR applied experiments # ############################# save_NMR_applied_experiment _Saveframe_category NMR_applied_experiment _Experiment_name ; 2D DQF COSY 2D TOCSY 2D NOESY ; save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 4.6 . pH temperature 298 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _Saveframe_category chemical_shift_reference 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 DSS H 1 "methyl protons" ppm 0.0 internal direct ? ? ? 1.0 DSS C 13 "methyl protons" ppm 0.0 . indirect ? ? ? 0.251449530 DSS N 15 "methyl protons" ppm 0.0 . indirect ? ? ? 0.101329118 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # Index Value Definition # # # # 1 Unique (geminal atoms and geminal methyl # # groups with identical chemical shifts # # are assumed to be assigned to # # stereospecific atoms) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups # # 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) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_chemical_shift_set_1 _Saveframe_category assigned_chemical_shifts loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name "Peptide YY" loop_ _Atom_shift_assign_ID _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 2 PRO HB3 H 2.30 . 2 2 2 PRO HA H 4.55 . 1 3 2 PRO HB2 H 1.94 . 2 4 2 PRO HG2 H 1.87 . 2 5 2 PRO HD2 H 3.21 . 2 6 3 ILE H H 8.33 . 1 7 3 ILE HA H 4.18 . 1 8 3 ILE HB H 1.78 . 1 9 3 ILE HG12 H 1.21 . 1 10 3 ILE HG2 H 0.89 . 1 11 3 ILE HG13 H 1.55 . 1 12 4 LYS H H 8.40 . 1 13 4 LYS HA H 3.54 . 1 14 4 LYS HG3 H 1.34 . 2 15 4 LYS HG2 H 0.91 . 2 16 4 LYS HB2 H 1.26 . 2 17 5 PRO HA H 4.40 . 1 18 5 PRO HB3 H 2.32 . 2 19 5 PRO HB2 H 1.93 . 2 20 5 PRO HG3 H 1.82 . 2 21 5 PRO HG2 H 1.76 . 2 22 5 PRO HD2 H 3.55 . 2 23 6 GLU HA H 4.14 . 1 24 6 GLU H H 8.47 . 1 25 6 GLU HG3 H 2.31 . 2 26 6 GLU HG2 H 2.40 . 2 27 6 GLU HB2 H 2.09 . 2 28 7 ALA H H 8.34 . 1 29 7 ALA HA H 3.58 . 1 30 7 ALA HB H 1.11 . 1 31 8 PRO HB3 H 2.10 . 2 32 8 PRO HA H 4.34 . 1 33 8 PRO HB2 H 1.77 . 2 34 8 PRO HG3 H 1.58 . 2 35 8 PRO HG2 H 1.56 . 2 36 8 PRO HD3 H 2.77 . 2 37 8 PRO HD2 H 2.81 . 2 38 9 GLY H H 8.31 . 1 39 9 GLY HA3 H 4.07 . 2 40 9 GLY HA2 H 3.86 . 2 41 10 GLU HA H 4.05 . 1 42 10 GLU H H 8.50 . 1 43 10 GLU HB3 H 2.03 . 2 44 10 GLU HB2 H 1.96 . 2 45 10 GLU HG3 H 2.32 . 2 46 11 ASP HA H 4.62 . 1 47 11 ASP H H 8.52 . 1 48 11 ASP HB2 H 2.71 . 2 49 12 ALA H H 7.30 . 1 50 12 ALA HA H 4.23 . 1 51 12 ALA HB H 1.33 . 1 52 13 SER HA H 4.56 . 1 53 13 SER H H 8.06 . 1 54 13 SER HB3 H 3.11 . 2 55 13 SER HB2 H 2.88 . 2 56 14 PRO HA H 4.25 . 1 57 14 PRO HB3 H 2.41 . 2 58 14 PRO HG3 H 2.04 . 2 59 14 PRO HG2 H 2.21 . 2 60 14 PRO HD3 H 3.94 . 2 61 14 PRO HD2 H 3.91 . 2 62 15 GLU H H 8.47 . 1 63 15 GLU HA H 4.22 . 1 64 15 GLU HB3 H 1.94 . 2 65 15 GLU HB2 H 1.83 . 2 66 15 GLU HG3 H 2.31 . 1 67 15 GLU HG2 H 2.31 . 1 68 16 GLU HA H 3.99 . 1 69 16 GLU H H 7.87 . 1 70 16 GLU HB3 H 2.27 . 2 71 16 GLU HB2 H 1.99 . 2 72 17 LEU H H 8.40 . 1 73 17 LEU HA H 3.95 . 1 74 17 LEU HB2 H 1.83 . 2 75 17 LEU HB3 H 1.55 . 2 76 17 LEU HD1 H 0.86 . 2 77 17 LEU HD2 H 0.82 . 2 78 18 ASN H H 8.40 . 1 79 18 ASN HA H 4.56 . 1 80 18 ASN HB3 H 2.94 . 2 81 18 ASN HB2 H 2.87 . 2 82 18 ASN HD21 H 7.66 . 1 83 18 ASN HD22 H 6.94 . 1 84 19 ARG H H 8.00 . 1 85 19 ARG HA H 4.13 . 1 86 19 ARG HB2 H 1.98 . 2 87 19 ARG HB3 H 1.93 . 2 88 19 ARG HG2 H 1.62 . 2 89 19 ARG HD2 H 3.27 . 2 90 19 ARG HD3 H 3.21 . 2 91 19 ARG HE H 7.47 . 1 92 19 ARG HG3 H 1.85 . 2 93 20 TYR H H 8.07 . 1 94 20 TYR HA H 4.38 . 1 95 20 TYR HB3 H 3.18 . 2 96 20 TYR HB2 H 3.00 . 2 97 20 TYR HD1 H 6.71 . 3 98 20 TYR HE1 H 6.51 . 3 99 21 TYR H H 8.72 . 1 100 21 TYR HA H 4.00 . 1 101 21 TYR HB3 H 3.12 . 2 102 21 TYR HB2 H 3.00 . 2 103 21 TYR HE1 H 6.86 . 3 104 21 TYR HD1 H 7.12 . 3 105 22 ALA H H 8.00 . 1 106 22 ALA HA H 4.13 . 1 107 22 ALA HB H 1.54 . 1 108 23 SER H H 8.23 . 1 109 23 SER HA H 4.34 . 1 110 23 SER HB3 H 4.08 . 2 111 23 SER HB2 H 3.97 . 2 112 24 LEU H H 8.79 . 1 113 24 LEU HA H 4.03 . 1 114 24 LEU HB3 H 1.65 . 2 115 24 LEU HB2 H 1.13 . 2 116 24 LEU HG H 1.50 . 1 117 24 LEU HD1 H 0.87 . 2 118 25 ARG H H 8.10 . 1 119 25 ARG HA H 3.96 . 1 120 25 ARG HB2 H 1.89 . 2 121 25 ARG HG2 H 1.75 . 2 122 25 ARG HG3 H 1.58 . 2 123 25 ARG HD2 H 3.14 . 2 124 26 HIS H H 7.87 . 1 125 26 HIS HA H 4.44 . 1 126 26 HIS HB3 H 3.38 . 2 127 26 HIS HB2 H 3.30 . 2 128 27 TYR H H 8.18 . 1 129 27 TYR HA H 4.13 . 1 130 27 TYR HB2 H 3.21 . 2 131 27 TYR HD1 H 7.00 . 3 132 27 TYR HE1 H 6.68 . 3 133 28 LEU H H 8.60 . 1 134 28 LEU HA H 3.85 . 1 135 28 LEU HB2 H 1.79 . 2 136 28 LEU HB3 H 1.45 . 2 137 28 LEU HG H 1.86 . 1 138 28 LEU HD1 H 0.88 . 2 139 29 ASN H H 7.98 . 1 140 29 ASN HA H 4.45 . 1 141 29 ASN HB3 H 2.88 . 2 142 29 ASN HB2 H 2.81 . 2 143 29 ASN HD21 H 7.58 . 1 144 29 ASN HD22 H 6.89 . 1 145 30 LEU HA H 4.10 . 1 146 30 LEU H H 7.72 . 1 147 30 LEU HB3 H 1.40 . 2 148 30 LEU HB2 H 1.72 . 2 149 30 LEU HG H 1.52 . 1 150 30 LEU HD1 H 0.76 . 2 151 31 VAL H H 7.88 . 1 152 31 VAL HA H 3.87 . 1 153 31 VAL HB H 1.96 . 1 154 31 VAL HG1 H 0.68 . 1 155 31 VAL HG2 H 0.62 . 1 156 32 THR H H 7.75 . 1 157 32 THR HA H 4.18 . 1 158 32 THR HB H 4.25 . 1 159 32 THR HG2 H 1.22 . 1 160 33 ARG H H 7.91 . 1 161 33 ARG HA H 4.23 . 1 162 33 ARG HB2 H 1.88 . 2 163 33 ARG HD2 H 3.16 . 2 164 33 ARG HB3 H 1.81 . 2 165 34 GLN HB3 H 2.03 . 2 166 34 GLN HB2 H 1.97 . 2 167 34 GLN H H 8.10 . 1 168 34 GLN HA H 4.20 . 1 169 35 ARG HA H 4.19 . 1 170 35 ARG H H 8.13 . 1 171 35 ARG HB2 H 1.67 . 2 172 35 ARG HG2 H 1.47 . 2 173 35 ARG HG3 H 1.39 . 2 174 35 ARG HD2 H 3.09 . 2 175 35 ARG HE H 7.12 . 1 stop_ save_