data_6856 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; 1H, 13C, and 15N assignments for UDP-N-acetylmuramyl-pentapeptide (PG-P) bound to Peptidoglycan associated lipoprotein (pal) from Haemophilus influenzae or free. ; _BMRB_accession_number 6856 _BMRB_flat_file_name bmr6856.str _Entry_type original _Submission_date 2005-10-08 _Accession_date 2005-10-10 _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 Parsons Lisa M. . 2 Orban John . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 44 "13C chemical shifts" 36 "15N chemical shifts" 7 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2006-04-24 original author . stop_ _Original_release_date 2006-04-24 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Peptidoglycan recognition by pal, an outer membrane lipoprotein' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 16475801 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Parsons Lisa M. . 2 Lin Florence . . 3 Orban John . . stop_ _Journal_abbreviation Biochemistry _Journal_volume 45 _Journal_issue 7 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 2122 _Page_last 2128 _Year 2006 _Details . loop_ _Keyword 'outer membrane lipoprotein' peptidoglycan stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name uyp _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label PG-P $UYP stop_ _System_molecular_weight 16236 _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state 'not present' loop_ _Biological_function structural stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_UYP _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common UDP-N-acetylmuramyl-L-Ala-D-Glu-m-Dap-D-Ala-D-Ala _Molecular_mass 1200 _Mol_thiol_state 'not present' loop_ _Biological_function structural stop_ _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 7 _Mol_residue_sequence XXAXXXX loop_ _Residue_seq_code _Residue_label 1 UDP 2 AMU 3 ALA 4 DGN 5 KCX 6 DAL 7 DAL stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_AMU _Saveframe_category polymer_residue _Mol_type D-saccharide _Name_common 'BETA-N-ACETYLMURAMIC ACID' _BMRB_code . _PDB_code AMU _Standard_residue_derivative . _Molecular_mass 293.270 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Wed Aug 31 14:02:52 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C1 C1 C . 0 . ? C2 C2 C . 0 . ? C3 C3 C . 0 . ? C4 C4 C . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? C7 C7 C . 0 . ? C8 C8 C . 0 . ? C9 C9 C . 0 . ? C10 C10 C . 0 . ? C11 C11 C . 0 . ? O1 O1 O . 0 . ? O3 O3 O . 0 . ? O4 O4 O . 0 . ? O5 O5 O . 0 . ? O6 O6 O . 0 . ? O7 O7 O . 0 . ? O10 O10 O . 0 . ? O11 O11 O . 0 . ? N2 N2 N . 0 . ? H1 H1 H . 0 . ? H2 H2 H . 0 . ? H3 H3 H . 0 . ? H4 H4 H . 0 . ? H5 H5 H . 0 . ? H61 H61 H . 0 . ? H62 H62 H . 0 . ? H81 H81 H . 0 . ? H82 H82 H . 0 . ? H83 H83 H . 0 . ? H9 H9 H . 0 . ? H111 H111 H . 0 . ? H112 H112 H . 0 . ? H113 H113 H . 0 . ? HO1 HO1 H . 0 . ? HO4 HO4 H . 0 . ? HO6 HO6 H . 0 . ? HO11 HO11 H . 0 . ? HN2 HN2 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 C1 C2 ? ? SING C1 O1 ? ? SING C1 O5 ? ? SING C1 H1 ? ? SING C2 C3 ? ? SING C2 N2 ? ? SING C2 H2 ? ? SING C3 C4 ? ? SING C3 O3 ? ? SING C3 H3 ? ? SING C4 C5 ? ? SING C4 O4 ? ? SING C4 H4 ? ? SING C5 C6 ? ? SING C5 O5 ? ? SING C5 H5 ? ? SING C6 O6 ? ? SING C6 H61 ? ? SING C6 H62 ? ? SING C7 C8 ? ? DOUB C7 O7 ? ? SING C7 N2 ? ? SING C8 H81 ? ? SING C8 H82 ? ? SING C8 H83 ? ? SING C9 C10 ? ? SING C9 C11 ? ? SING C9 O3 ? ? SING C9 H9 ? ? DOUB C10 O10 ? ? SING C10 O11 ? ? SING C11 H111 ? ? SING C11 H112 ? ? SING C11 H113 ? ? SING O1 HO1 ? ? SING O4 HO4 ? ? SING O6 HO6 ? ? SING O11 HO11 ? ? SING N2 HN2 ? ? stop_ save_ save_chem_comp_DGN _Saveframe_category polymer_residue _Mol_type 'D-peptide linking' _Name_common D-GLUTAMINE _BMRB_code . _PDB_code DGN _Standard_residue_derivative . _Molecular_mass 146.144 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Wed Aug 31 14:04:33 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? CA CA C . 0 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? CD CD C . 0 . ? OE1 OE1 O . 0 . ? NE2 NE2 N . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HA HA H . 0 . ? HXT HXT H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG2 HG2 H . 0 . ? HG3 HG3 H . 0 . ? HE21 HE21 H . 0 . ? HE22 HE22 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 ? ? SING N H ? ? SING N H2 ? ? SING CA C ? ? SING CA CB ? ? SING CA HA ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG CD ? ? SING CG HG2 ? ? SING CG HG3 ? ? DOUB CD OE1 ? ? SING CD NE2 ? ? SING NE2 HE21 ? ? SING NE2 HE22 ? ? stop_ save_ save_chem_comp_KCX _Saveframe_category polymer_residue _Mol_type 'L-peptide linking' _Name_common 'LYSINE NZ-CARBOXYLIC ACID' _BMRB_code . _PDB_code KCX _Standard_residue_derivative . _Molecular_mass 190.197 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Wed Aug 31 14:07:08 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? CA CA C . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? CD CD C . 0 . ? CE CE C . 0 . ? NZ NZ N . 0 . ? C C C . 0 . ? O O O . 0 . ? CX CX C . 0 . ? OXT OXT O . 0 . ? OQ1 OQ1 O . 0 . ? OQ2 OQ2 O . 0 . ? H H H . 0 . ? HN2 HN2 H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG2 HG2 H . 0 . ? HG3 HG3 H . 0 . ? HD2 HD2 H . 0 . ? HD3 HD3 H . 0 . ? HE2 HE2 H . 0 . ? HE3 HE3 H . 0 . ? HZ HZ H . 0 . ? HXT HXT H . 0 . ? HQ2 HQ2 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 ? ? SING N H ? ? SING N HN2 ? ? SING CA CB ? ? SING CA C ? ? SING CA HA ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG CD ? ? SING CG HG2 ? ? SING CG HG3 ? ? SING CD CE ? ? SING CD HD2 ? ? SING CD HD3 ? ? SING CE NZ ? ? SING CE HE2 ? ? SING CE HE3 ? ? SING NZ CX ? ? SING NZ HZ ? ? DOUB C O ? ? SING C OXT ? ? DOUB CX OQ1 ? ? SING CX OQ2 ? ? SING OXT HXT ? ? SING OQ2 HQ2 ? ? stop_ save_ save_chem_comp_DAL _Saveframe_category polymer_residue _Mol_type 'D-peptide linking' _Name_common D-ALANINE _BMRB_code . _PDB_code DAL _Standard_residue_derivative . _Molecular_mass 89.093 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Wed Aug 31 14:10:02 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? CA CA C . 0 . ? CB CB C . 0 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HA HA H . 0 . ? HB1 HB1 H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HXT HXT 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 ? ? SING N H ? ? SING N H2 ? ? SING CA CB ? ? SING CA C ? ? SING CA HA ? ? SING CB HB1 ? ? SING CB HB2 ? ? SING CB HB3 ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $UYP 'Escherichia coli' 562 Eubacteria . Escherichia coli 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 $UYP 'recombinant technology' 'E. coli' . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_UYPfree _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $UYP 0.8 mM '[U-13C; U-15N]' NaCl 50 mM . PO4 50 mM . stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_HCCHTOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name HCCHTOCSY _Sample_label $UYPfree save_ save_C13-HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name C13-HSQC _Sample_label $UYPfree save_ save_2D-TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name 2D-TOCSY _Sample_label $UYPfree save_ save_2D_H-C'_plane_of_HNCO_4 _Saveframe_category NMR_applied_experiment _Experiment_name "2D H-C' plane of HNCO" _Sample_label $UYPfree save_ ####################### # Sample conditions # ####################### save_conditions_1 _Saveframe_category sample_conditions _Details '50 mM NaCl, 50 mM PO4' loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.7 0.1 pH temperature 298 1 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_referencing _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 _Indirect_shift_ratio_citation_label _Correction_value_citation_label water H 1 protons ppm 4.8 internal direct . . . 1.0 $entry_citation $entry_citation 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_UYP_free _Saveframe_category assigned_chemical_shifts _Details 'UDP-N-acetylmuramyl-L-Ala-D-Glu-m-Dap-D-Ala-D-Ala alone' loop_ _Sample_label $UYPfree stop_ _Sample_conditions_label $conditions_1 _Chem_shift_reference_set_label $chemical_shift_referencing _Mol_system_component_name PG-P _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 UDP C5 C 105.5 0.3 1 2 1 1 UDP H5 H 5.97 0.03 1 3 1 1 UDP C6 C 144.2 0.3 1 4 1 1 UDP H6 H 7.96 0.03 1 5 1 1 UDP C1' C 91.4 0.3 1 6 1 1 UDP H1' H 5.98 0.03 1 7 1 1 UDP C2' C 76.2 0.3 1 8 1 1 UDP H2' H 4.37 0.03 1 9 1 1 UDP C3' C 72.5 0.3 1 10 1 1 UDP H3' H 4.36 0.03 1 11 1 1 UDP C4' C 86.0 0.3 1 12 1 1 UDP H4' H 4.28 0.03 1 13 1 1 UDP C5' C 67.8 0.3 1 14 1 1 UDP H5' H 4.19 0.03 2 15 1 1 UDP H5'' H 4.19 0.03 2 16 2 2 AMU C1 C 97.4 0.3 1 17 2 2 AMU H1 H 5.47 0.03 1 18 2 2 AMU C2 C 56.1 0.3 1 19 2 2 AMU H2 H 4.13 0.03 1 20 2 2 AMU N2 N 121.8 0.4 1 21 2 2 AMU HH2 H 8.49 0.03 1 22 2 2 AMU C3 C 82.7 0.3 1 23 2 2 AMU H3 H 3.79 0.03 1 24 2 2 AMU C4 C 70.8 0.3 1 25 2 2 AMU H4 H 3.65 0.03 1 26 2 2 AMU C5 C 75.8 0.3 1 27 2 2 AMU H5 H 3.95 0.03 1 28 2 2 AMU C6 C 63.2 0.3 1 29 2 2 AMU H61 H 3.86 0.03 2 30 2 2 AMU H62 H 3.86 0.03 2 31 2 2 AMU C7 C 177 0.3 1 32 2 2 AMU C8 C 25.0 0.3 1 33 2 2 AMU H8 H 2.02 0.03 2 34 2 2 AMU C9 C 80.8 0.3 1 35 2 2 AMU H9 H 4.23 0.03 1 36 2 2 AMU C10 C 178.6 0.3 1 37 2 2 AMU C11 C 21.5 0.3 1 38 2 2 AMU H11 H 1.42 0.03 2 39 3 3 ALA H H 7.98 0.03 1 40 3 3 ALA HA H 4.12 0.03 1 41 3 3 ALA HB H 1.34 0.03 1 42 3 3 ALA C C 176.8 0.3 1 43 3 3 ALA CA C 53.9 0.3 1 44 3 3 ALA CB C 20.3 0.3 1 45 3 3 ALA N N 123.2 0.4 1 46 4 4 DGN H H 7.90 0.03 1 47 4 4 DGN HA H 4.16 0.03 1 48 4 4 DGN HB2 H 2.14 0.03 2 49 4 4 DGN HB3 H 1.90 0.03 2 50 4 4 DGN HG2 H 2.31 0.03 2 51 4 4 DGN HG3 H 2.31 0.03 2 52 4 4 DGN C C 178.5 0.3 1 53 4 4 DGN CA C 57.2 0.3 1 54 4 4 DGN CB C 30.8 0.3 1 55 4 4 DGN CG C 34.5 0.3 1 56 4 4 DGN N N 123.2 0.4 1 57 5 5 KCX H H 8.28 0.03 1 58 5 5 KCX HA H 3.74 0.03 1 59 5 5 KCX HB2 H 1.93 0.03 2 60 5 5 KCX HB3 H 1.84 0.03 2 61 5 5 KCX HG2 H 1.47 0.03 2 62 5 5 KCX HG3 H 1.47 0.03 2 63 5 5 KCX HD2 H 1.83 0.03 2 64 5 5 KCX HD3 H 1.79 0.03 2 65 5 5 KCX HE H 4.23 0.03 1 66 5 5 KCX HZ H 8.28 0.03 2 67 5 5 KCX C C 176.9 0.3 1 68 5 5 KCX CA C 57.5 0.3 1 69 5 5 KCX CB C 32.9 0.3 1 70 5 5 KCX CG C 23.8 0.3 1 71 5 5 KCX CD C 33.4 0.3 1 72 5 5 KCX CE C 57.34 0.3 1 73 5 5 KCX N N 126.6 0.4 1 74 5 5 KCX NZ N 117.4 0.4 1 75 6 6 DAL H H 8.35 0.03 1 76 6 6 DAL HA H 4.3 0.03 1 77 6 6 DAL HB H 1.44 0.03 2 78 6 6 DAL C C 176.4 0.3 1 79 6 6 DAL CA C 52.4 0.3 1 80 6 6 DAL CB C 19.8 0.3 1 81 6 6 DAL N N 124.8 0.4 1 82 7 7 DAL H H 7.93 0.03 1 83 7 7 DAL HA H 4.30 0.03 1 84 7 7 DAL HB H 1.38 0.03 2 85 7 7 DAL CA C 52.6 0.3 1 86 7 7 DAL CB C 19.4 0.3 1 87 7 7 DAL N N 129.7 0.4 1 stop_ save_