data_6557 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution Conformation of adr subtype HBV Pre-S2 Epitope ; _BMRB_accession_number 6557 _BMRB_flat_file_name bmr6557.str _Entry_type original _Submission_date 2005-03-18 _Accession_date 2005-03-23 _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 Chi S.-W. . . 2 Han K.-H. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 coupling_constants 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 128 "coupling constants" 15 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2007-11-14 update BMRB 'complete the entry citation' 2006-08-11 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Solution conformation of an immunodominant epitope in the hepatitis B virus preS2 surface antigen ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 16872688 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Chi S.-W. . . 2 Kim D.-H. . . 3 Kim J.-S. . . 4 Lee M.-K. . . 5 Han K.-H. . . stop_ _Journal_abbreviation 'Antiviral Res.' _Journal_volume 72 _Journal_issue 3 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 207 _Page_last 215 _Year 2006 _Details . loop_ _Keyword 'Helix turn helix' stop_ save_ ################################## # Molecular system description # ################################## save_system_antigen _Saveframe_category molecular_system _Mol_system_name 'preS2 surface antigen' _Abbreviation_common 'preS2 surface antigen' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'Major surface antigen' $antigen 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_antigen _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'Major surface antigen' _Abbreviation_common 'Major surface antigen' _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 23 _Mol_residue_sequence ; NSTTFHQALLDPRVRGLYFP AGG ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 123 ASN 2 124 SER 3 125 THR 4 126 THR 5 127 PHE 6 128 HIS 7 129 GLN 8 130 ALA 9 131 LEU 10 132 LEU 11 133 ASP 12 134 PRO 13 135 ARG 14 136 VAL 15 137 ARG 16 138 GLY 17 139 LEU 18 140 TYR 19 141 PHE 20 142 PRO 21 143 ALA 22 144 GLY 23 145 GLY stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-01-28 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 PDB 1A7L "Dominant B-Cell Epitope From The Pres2 Region Of Hepatitis B Virus In The Form Of An Inserted Peptide Segment In Maltodextrin-B" 56.52 389 100.00 100.00 3.71e+00 PDB 1IUD "Maltodextrin-Binding Protein InsertionDELETION MUTANT WITH An Inserted B-Cell Epitope From The Pres2 Region Of Hepatitis B Viru" 56.52 380 100.00 100.00 5.07e+00 PDB 1WZ4 "Solution Conformation Of Adr Subtype Hbv Pre-S2 Epitope" 100.00 23 100.00 100.00 3.56e-07 DBJ BAA00944 "envelope proteins [Hepatitis B virus]" 100.00 281 100.00 100.00 1.16e-06 DBJ BAA02359 "surface antigen precursor [Hepatitis B virus]" 100.00 400 100.00 100.00 3.55e-06 DBJ BAA04920 "HBV surface proteins [Hepatitis B virus]" 100.00 242 100.00 100.00 1.83e-06 DBJ BAA04924 "HBV surface proteins [Hepatitis B virus]" 100.00 400 100.00 100.00 3.62e-06 DBJ BAA04928 "HBV surface proteins [Hepatitis B virus]" 100.00 400 100.00 100.00 3.31e-06 EMBL CAA25747 "unnamed protein product [Hepatitis B virus]" 100.00 445 100.00 100.00 4.24e-06 EMBL CAA36251 "S2/S [Hepatitis B virus]" 100.00 102 100.00 100.00 4.20e-07 EMBL CAA37114 "unnamed protein product [Hepatitis B virus]" 100.00 445 100.00 100.00 3.84e-06 EMBL CAD34587 "surface antigen [Hepatitis B virus]" 100.00 220 100.00 100.00 1.47e-06 EMBL CAR70008 "large surface protein [Hepatitis B virus]" 100.00 400 100.00 100.00 3.31e-06 GB AAB36406 "envelope [Hepatitis B virus]" 100.00 400 100.00 100.00 3.48e-06 GB AAB88749 "surface antigen [Hepatitis B virus]" 95.65 277 100.00 100.00 8.70e-06 GB AAB88752 "surface antigen [Hepatitis B virus]" 95.65 277 100.00 100.00 8.88e-06 GB AAF15903 "large envelope protein [Hepatitis B virus]" 100.00 400 100.00 100.00 3.22e-06 GB AAF82724 "large surface antigen [Hepatitis B virus]" 100.00 400 100.00 100.00 3.28e-06 PRF 1011236B "antigen HBsAg,surface" 100.00 400 100.00 100.00 3.38e-06 REF YP_355333 "large S protein [Hepatitis B virus]" 100.00 400 100.00 100.00 3.62e-06 REF YP_355334 "middle S protein [Hepatitis B virus]" 100.00 281 100.00 100.00 1.17e-06 SP P03140 "RecName: Full=Large envelope protein; AltName: Full=L glycoprotein; AltName: Full=L-HBsAg; Short=LHB; AltName: Full=Large S pro" 100.00 400 100.00 100.00 3.38e-06 SP P12934 "RecName: Full=Large envelope protein; AltName: Full=L glycoprotein; AltName: Full=L-HBsAg; Short=LHB; AltName: Full=Large S pro" 100.00 400 100.00 100.00 3.76e-06 SP P31868 "RecName: Full=Large envelope protein; AltName: Full=L glycoprotein; AltName: Full=L-HBsAg; Short=LHB; AltName: Full=Large S pro" 100.00 400 100.00 100.00 3.55e-06 SP Q76R62 "RecName: Full=Large envelope protein; AltName: Full=L glycoprotein; AltName: Full=L-HBsAg; Short=LHB; AltName: Full=Large S pro" 100.00 400 100.00 100.00 3.62e-06 SP Q81162 "RecName: Full=Large envelope protein; AltName: Full=L glycoprotein; AltName: Full=L-HBsAg; Short=LHB; AltName: Full=Large S pro" 100.00 389 100.00 100.00 2.97e-06 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $antigen 'Hepatitis B virus' 10407 Viruses . Orthohepadnavirus 'Hepatitis B virus' 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 $antigen '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 $antigen 5 mM . CD3OH 95 % . H2O 5 % . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $antigen 5 mM . D2O 100 % . stop_ save_ ############################ # Computer software used # ############################ save_VNMR _Saveframe_category software _Name VNMR _Version 6.1B loop_ _Task collection stop_ _Details . save_ save_FELIX _Saveframe_category software _Name FELIX _Version 98.0 loop_ _Task processing stop_ _Details . save_ save_DISCOVER _Saveframe_category software _Name DISCOVER _Version 2.98 loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model UNITY _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label . save_ save_2D_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label . save_ save_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label . save_ save_PE-COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name PE-COSY _Sample_label . save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_5 _Saveframe_category NMR_applied_experiment _Experiment_name PE-COSY _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 3.85 . pH temperature 288 . K 'ionic strength' 0 . . pressure 1 . atm 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 DSS H 1 'methyl protons' ppm 0.0 . indirect . . . 1.0 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_chemical_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 'Major surface antigen' _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 ASN HA H 4.250 0.01 1 2 . 1 ASN HB2 H 3.300 0.01 2 3 . 1 ASN HB3 H 3.060 0.01 2 4 . 2 SER H H 9.130 0.01 1 5 . 2 SER HA H 4.260 0.01 1 6 . 2 SER HB2 H 3.900 0.01 1 7 . 2 SER HB3 H 3.900 0.01 1 8 . 3 THR H H 7.910 0.01 1 9 . 3 THR HA H 4.090 0.01 1 10 . 3 THR HB H 4.250 0.01 1 11 . 3 THR HG2 H 1.180 0.01 1 12 . 4 THR H H 8.310 0.01 1 13 . 4 THR HA H 4.070 0.01 1 14 . 4 THR HB H 4.170 0.01 1 15 . 4 THR HG2 H 1.190 0.01 1 16 . 5 PHE H H 8.220 0.01 1 17 . 5 PHE HA H 4.260 0.01 1 18 . 5 PHE HB2 H 3.120 0.01 2 19 . 5 PHE HB3 H 3.040 0.01 2 20 . 5 PHE HD1 H 7.020 0.01 1 21 . 5 PHE HD2 H 7.020 0.01 1 22 . 5 PHE HE1 H 7.110 0.01 1 23 . 5 PHE HE2 H 7.110 0.01 1 24 . 5 PHE HZ H 7.060 0.01 3 25 . 6 HIS H H 8.090 0.01 1 26 . 6 HIS HA H 4.100 0.01 1 27 . 6 HIS HB2 H 3.310 0.01 1 28 . 6 HIS HB3 H 3.310 0.01 1 29 . 6 HIS HD2 H 7.350 0.01 1 30 . 6 HIS HE1 H 8.680 0.01 1 31 . 7 GLN H H 8.280 0.01 1 32 . 7 GLN HA H 3.920 0.01 1 33 . 7 GLN HB2 H 2.190 0.01 2 34 . 7 GLN HB3 H 2.020 0.01 2 35 . 7 GLN HG2 H 2.460 0.01 2 36 . 7 GLN HG3 H 2.310 0.01 2 37 . 7 GLN HE21 H 6.740 0.01 1 38 . 7 GLN HE22 H 7.540 0.01 1 39 . 8 ALA H H 8.130 0.01 1 40 . 8 ALA HA H 4.020 0.01 1 41 . 8 ALA HB H 1.380 0.01 1 42 . 9 LEU H H 7.420 0.01 1 43 . 9 LEU HA H 3.930 0.01 1 44 . 9 LEU HB2 H 1.630 0.01 2 45 . 9 LEU HB3 H 1.340 0.01 2 46 . 9 LEU HG H 1.470 0.01 1 47 . 9 LEU HD1 H 0.600 0.01 1 48 . 9 LEU HD2 H 0.600 0.01 1 49 . 10 LEU H H 7.380 0.01 1 50 . 10 LEU HA H 4.160 0.01 1 51 . 10 LEU HB2 H 1.700 0.01 2 52 . 10 LEU HB3 H 1.500 0.01 2 53 . 10 LEU HG H 1.680 0.01 1 54 . 10 LEU HD1 H 0.800 0.01 1 55 . 10 LEU HD2 H 0.770 0.01 1 56 . 11 ASP H H 7.810 0.01 1 57 . 11 ASP HA H 4.840 0.01 1 58 . 11 ASP HB2 H 3.100 0.01 2 59 . 11 ASP HB3 H 2.610 0.01 2 60 . 12 PRO HA H 4.240 0.01 1 61 . 12 PRO HB2 H 2.320 0.01 2 62 . 12 PRO HB3 H 1.940 0.01 2 63 . 12 PRO HG2 H 2.000 0.01 1 64 . 12 PRO HG3 H 2.000 0.01 1 65 . 12 PRO HD2 H 4.030 0.01 2 66 . 12 PRO HD3 H 3.880 0.01 2 67 . 13 ARG H H 8.430 0.01 1 68 . 13 ARG HA H 4.030 0.01 1 69 . 13 ARG HB2 H 1.840 0.01 1 70 . 13 ARG HB3 H 1.840 0.01 1 71 . 13 ARG HG2 H 1.680 0.01 2 72 . 13 ARG HD2 H 3.210 0.01 2 73 . 13 ARG HD3 H 3.100 0.01 2 74 . 14 VAL H H 7.470 0.01 1 75 . 14 VAL HA H 3.910 0.01 1 76 . 14 VAL HB H 2.320 0.01 1 77 . 14 VAL HG1 H 0.950 0.01 1 78 . 14 VAL HG2 H 0.930 0.01 1 79 . 15 ARG H H 8.010 0.01 1 80 . 15 ARG HA H 4.090 0.01 1 81 . 15 ARG HB2 H 1.920 0.01 2 82 . 15 ARG HB3 H 1.840 0.01 2 83 . 15 ARG HG2 H 1.680 0.01 2 84 . 15 ARG HD2 H 3.180 0.01 1 85 . 15 ARG HD3 H 3.180 0.01 1 86 . 16 GLY H H 8.110 0.01 1 87 . 16 GLY HA2 H 3.840 0.01 2 88 . 16 GLY HA3 H 3.730 0.01 2 89 . 17 LEU H H 7.590 0.01 1 90 . 17 LEU HA H 4.120 0.01 1 91 . 17 LEU HB2 H 1.550 0.01 2 92 . 17 LEU HB3 H 1.230 0.01 2 93 . 17 LEU HG H 1.540 0.01 1 94 . 17 LEU HD1 H 0.820 0.01 1 95 . 17 LEU HD2 H 0.740 0.01 1 96 . 18 TYR H H 7.540 0.01 1 97 . 18 TYR HA H 4.280 0.01 1 98 . 18 TYR HB2 H 2.660 0.01 2 99 . 18 TYR HB3 H 2.610 0.01 2 100 . 18 TYR HD1 H 6.980 0.01 1 101 . 18 TYR HD2 H 6.980 0.01 1 102 . 18 TYR HE1 H 6.600 0.01 1 103 . 18 TYR HE2 H 6.600 0.01 1 104 . 19 PHE H H 8.050 0.01 1 105 . 19 PHE HA H 4.870 0.01 1 106 . 19 PHE HB2 H 3.050 0.01 2 107 . 19 PHE HB3 H 2.850 0.01 2 108 . 19 PHE HD1 H 7.240 0.01 1 109 . 19 PHE HD2 H 7.240 0.01 1 110 . 19 PHE HE1 H 7.200 0.01 1 111 . 19 PHE HE2 H 7.200 0.01 1 112 . 19 PHE HZ H 7.130 0.01 3 113 . 20 PRO HA H 4.390 0.01 1 114 . 20 PRO HB2 H 2.200 0.01 2 115 . 20 PRO HB3 H 1.900 0.01 2 116 . 20 PRO HG2 H 1.880 0.01 1 117 . 20 PRO HG3 H 1.880 0.01 1 118 . 20 PRO HD2 H 3.410 0.01 1 119 . 20 PRO HD3 H 3.410 0.01 1 120 . 21 ALA H H 8.380 0.01 1 121 . 21 ALA HA H 4.250 0.01 1 122 . 21 ALA HB H 1.360 0.01 1 123 . 22 GLY H H 8.220 0.01 1 124 . 22 GLY HA2 H 3.930 0.01 2 125 . 22 GLY HA3 H 3.810 0.01 2 126 . 23 GLY H H 8.070 0.01 1 127 . 23 GLY HA2 H 3.840 0.01 1 128 . 23 GLY HA3 H 3.840 0.01 1 stop_ save_ ######################## # Coupling constants # ######################## save_J-values_set_1 _Saveframe_category coupling_constants _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Spectrometer_frequency_1H 500 _Mol_system_component_name 'Major surface antigen' _Text_data_format . _Text_data . loop_ _Coupling_constant_ID _Coupling_constant_code _Atom_one_residue_seq_code _Atom_one_residue_label _Atom_one_name _Atom_two_residue_seq_code _Atom_two_residue_label _Atom_two_name _Coupling_constant_value _Coupling_constant_min_value _Coupling_constant_max_value _Coupling_constant_value_error 1 3JHNHA 2 SER H 2 SER HA 4.4 . . 0.01 2 3JHNHA 3 THR H 3 THR HA 6.0 . . 0.01 3 3JHNHA 4 THR H 4 THR HA 5.2 . . 0.01 4 3JHNHA 5 PHE H 5 PHE HA 4.7 . . 0.01 5 3JHNHA 6 HIS H 6 HIS HA 5.2 . . 0.01 6 3JHNHA 7 GLN H 7 GLN HA 5.0 . . 0.01 7 3JHNHA 8 ALA H 8 ALA HA 4.6 . . 0.01 8 3JHNHA 9 LEU H 9 LEU HA 5.6 . . 0.01 9 3JHNHA 10 LEU H 10 LEU HA 7.5 . . 0.01 10 3JHNHA 13 ARG H 13 ARG HA 6.6 . . 0.01 11 3JHNHA 14 VAL H 14 VAL HA 7.9 . . 0.01 12 3JHNHA 15 ARG H 15 ARG HA 4.6 . . 0.01 13 3JHNHA 17 LEU H 17 LEU HA 6.9 . . 0.01 14 3JHNHA 18 TYR H 18 TYR HA 8.4 . . 0.01 15 3JHNHA 21 ALA H 21 ALA HA 6.1 . . 0.01 stop_ save_