data_5301 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Principles of Mucin Architecture: Structural Studies on Synthetic Glycopeptides Bearing Clustered Mono-,Di, Tri-, and Hexasacchraride Glycodomains ; _BMRB_accession_number 5301 _BMRB_flat_file_name bmr5301.str _Entry_type original _Submission_date 2002-02-25 _Accession_date 2002-02-25 _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 Coltart D. M. . 2 Royyuru A. K. . 3 Williams L. J. . 4 Glunz P. W. . 5 Sames D. . . 6 Kuduk S. D. . 7 Schwarz J. B. . 8 Chen X.-T. . . 9 Danishefsky S. D. . 10 Live D. H. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 20 "13C chemical shifts" 14 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-07-17 update BMRB 'Updating non-standard residue' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Principles of Mucin Architecture: Structural Studies on Synthetic Glycopeptides Bearing Clustered Mono-,Di, Tri-, and Hexasacchraride Glycodomains ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 22166449 _PubMed_ID 12175243 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Coltart D. M. . 2 Royyuru A. K. . 3 Williams L. J. . 4 Glunz P. W. . 5 Sames D. . . 6 Kuduk S. D. . 7 Schwarz J. B. . 8 Chen X.-T. . . 9 Danishefsky S. D. . 10 Live D. H. . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_volume 124 _Journal_issue 33 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 9833 _Page_last 9844 _Year 2002 _Details . loop_ _Keyword CD43 Leukosialin 'Mucin glycoprotein' stop_ save_ ################################## # Molecular system description # ################################## save_system_CD43 _Saveframe_category molecular_system _Mol_system_name 'Leukosialin (CD43) fragment' _Abbreviation_common CD43 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'Leukosialin (CD43) fragment' $CD43 'N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE, 1' $A2G 'N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE, 2' $A2G 'N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE, 3' $A2G 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_CD43 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'Leukosialin (CD43) fragment' _Abbreviation_common CD43 _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 6 _Mol_residue_sequence XSTTAV loop_ _Residue_seq_code _Residue_label 1 ACE 2 SER 3 THR 4 THR 5 ALA 6 VAL stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_ACE _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common 'ACETYL GROUP' _BMRB_code . _PDB_code ACE _Standard_residue_derivative . _Molecular_mass 44.053 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Thu Jul 14 16:15:33 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C C C . 0 . ? O O O . 0 . ? CH3 CH3 C . 0 . ? H H H . 0 . ? H1 H1 H . 0 . ? H2 H2 H . 0 . ? H3 H3 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 DOUB C O ? ? SING C CH3 ? ? SING C H ? ? SING CH3 H1 ? ? SING CH3 H2 ? ? SING CH3 H3 ? ? stop_ save_ ############# # Ligands # ############# save_A2G _Saveframe_category ligand _Mol_type "non-polymer (saccharide)" _Name_common "A2G (N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE)" _BMRB_code . _PDB_code A2G _Molecular_mass 221.208 _Mol_charge 0 _Mol_paramagnetic . _Mol_aromatic no _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Thu Jul 21 16:53:29 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons O O O . 0 . ? C1 C1 C . 0 . ? O1 O1 O . 0 . ? C2 C2 C . 0 . ? N2 N2 N . 0 . ? C3 C3 C . 0 . ? O3 O3 O . 0 . ? C4 C4 C . 0 . ? O4 O4 O . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? O6 O6 O . 0 . ? C7 C7 C . 0 . ? O7 O7 O . 0 . ? C8 C8 C . 0 . ? H1 H1 H . 0 . ? HO1 HO1 H . 0 . ? H2 H2 H . 0 . ? HN2 HN2 H . 0 . ? H3 H3 H . 0 . ? HO3 HO3 H . 0 . ? H4 H4 H . 0 . ? HO4 HO4 H . 0 . ? H5 H5 H . 0 . ? H6 H6 H . 0 . ? H8 H8 H . 0 . ? H8A H8A H . 0 . ? H8B H8B H . 0 . ? H14 H14 H . 0 . ? H15 H15 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 O C5 ? ? SING C1 O ? ? SING C1 C2 ? ? SING C1 H1 ? ? SING O1 C1 ? ? SING O1 HO1 ? ? SING C2 C3 ? ? SING C2 H2 ? ? SING N2 C2 ? ? SING N2 HN2 ? ? SING C3 C4 ? ? SING C3 O3 ? ? SING C3 H3 ? ? SING O3 HO3 ? ? SING C4 O4 ? ? SING C4 H4 ? ? SING O4 HO4 ? ? SING C5 C4 ? ? SING C5 C6 ? ? SING C5 H5 ? ? SING C6 O6 ? ? SING C6 H6 ? ? SING C7 N2 ? ? DOUB O7 C7 ? ? SING C8 C7 ? ? SING C8 H8 ? ? SING C8 H8A ? ? SING C8 H8B ? ? SING C6 H14 ? ? SING O6 H15 ? ? 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 $CD43 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 $CD43 'chemical synthesis' . . . . . 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 _Isotopic_labeling $CD43 10 mM . $A2G 30 mM . H2O 90 % . D2O 10 % . stop_ save_ ############################ # Computer software used # ############################ save_VNMR _Saveframe_category software _Name VNMR _Version 6.1 loop_ _Task collection 'data analysis' stop_ _Details 'Varian Inc.' save_ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version 2.1 loop_ _Task 'data analysis' stop_ _Details Delaglio save_ save_X-PLOR _Saveframe_category software _Name X-PLOR _Version 98 loop_ _Task refinement stop_ _Details Brunger/MSI save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 800 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_1 save_ save_3D_TOCSY-NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '3D TOCSY-NOESY' _Sample_label $sample_1 save_ save_NMR_applied_experiment _Saveframe_category NMR_applied_experiment _Experiment_name . _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 4.5 . n/a pressure 1 . atm temperature 291 . 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_citation_label _Correction_value_citation_label . C 13 . ppm . . . . . . $entry_citation $entry_citation . H 1 . ppm . . . . . . $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_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'Leukosialin (CD43) fragment' _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 SER H H 8.500 0.002 1 2 . 2 SER HA H 4.823 0.002 1 3 . 2 SER HB2 H 3.878 0.002 2 4 . 2 SER HB3 H 4.087 0.002 2 5 . 2 SER CA C 56.275 0.015 1 6 . 2 SER CB C 70.580 0.015 1 7 . 3 THR H H 8.821 0.002 1 8 . 3 THR HA H 4.821 0.002 1 9 . 3 THR HB H 4.396 0.002 1 10 . 3 THR HG2 H 1.353 0.002 1 11 . 3 THR CA C 59.775 0.015 1 12 . 3 THR CB C 81.526 0.015 1 13 . 3 THR CG2 C 21.198 0.015 1 14 . 4 THR H H 8.884 0.002 1 15 . 4 THR HA H 4.561 0.002 1 16 . 4 THR HB H 4.273 0.002 1 17 . 4 THR HG2 H 1.291 0.002 1 18 . 4 THR CA C 59.532 0.015 1 19 . 4 THR CB C 79.731 0.015 1 20 . 4 THR CG2 C 21.383 0.015 1 21 . 5 ALA H H 8.398 0.002 1 22 . 5 ALA HA H 4.391 0.002 1 23 . 5 ALA HB H 1.375 0.002 1 24 . 5 ALA CA C 51.372 0.015 1 25 . 5 ALA CB C 20.733 0.015 1 26 . 6 VAL H H 7.785 0.002 1 27 . 6 VAL HA H 3.917 0.002 1 28 . 6 VAL HB H 2.031 0.002 1 29 . 6 VAL HG1 H 0.891 0.002 2 30 . 6 VAL HG2 H 0.898 0.002 2 31 . 6 VAL CA C 63.760 0.015 1 32 . 6 VAL CB C 32.906 0.015 1 33 . 6 VAL CG1 C 21.489 0.015 2 34 . 6 VAL CG2 C 20.485 0.015 2 stop_ save_