data_7422 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Pseudo Contact shifts and RDCs of Galectin-3 with C-terminal LBT tagged at a proton frequency of 600MHz. ; _BMRB_accession_number 7422 _BMRB_flat_file_name bmr7422.str _Entry_type original _Submission_date 2008-04-01 _Accession_date 2008-04-01 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details ; For pseudo contact shifts and RDCs measurement, Dysprosium is used as paramagnetic metal ion while diamagnetic Lutetium is used as diamagnetic reference ; loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Zhuang Tiandi . . 2 Lee Han-seung . . 3 Imperiali Barbara . . 4 Prestegard James . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 34 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-06-30 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 15705 'Complex with paramagnetic Dysprosium' stop_ _Original_release_date 2008-06-30 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structure determination of a Galectin-3-carbohydrate complex using paramagnetism-based NMR constraints' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 18413860 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Zhuang Tiandi . . 2 Lee Han-seung . . 3 Imperiali Barbara . . 4 Prestegard James H. . stop_ _Journal_abbreviation 'Protein Sci.' _Journal_volume 17 _Journal_issue 7 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1220 _Page_last 1231 _Year 2008 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name Galectin-3-LBT _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label Galectin-3-LBT $Galectin-3-LBT 'LUTETIUM ion' $LU 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_Galectin-3-LBT _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common Galectin-3-LBT _Molecular_mass . _Mol_thiol_state 'all free' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 155 _Mol_residue_sequence ; MLIVPYNLPLPGGVVPRMLI TILGTVKPNANRIALDFQRG NDVAFHFNPRFNERNRRVIV CNTKLDNNWGREERQSVFPF ESGKPFKIQVLVEPDHFKVA VNDAHLLQYNHRVKKLNEIS KLGISGDIDLTSASYTMIYI DTNNDGWYEGDELLA ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 113 MET 2 114 LEU 3 115 ILE 4 116 VAL 5 117 PRO 6 118 TYR 7 119 ASN 8 120 LEU 9 121 PRO 10 122 LEU 11 123 PRO 12 124 GLY 13 125 GLY 14 126 VAL 15 127 VAL 16 128 PRO 17 129 ARG 18 130 MET 19 131 LEU 20 132 ILE 21 133 THR 22 134 ILE 23 135 LEU 24 136 GLY 25 137 THR 26 138 VAL 27 139 LYS 28 140 PRO 29 141 ASN 30 142 ALA 31 143 ASN 32 144 ARG 33 145 ILE 34 146 ALA 35 147 LEU 36 148 ASP 37 149 PHE 38 150 GLN 39 151 ARG 40 152 GLY 41 153 ASN 42 154 ASP 43 155 VAL 44 156 ALA 45 157 PHE 46 158 HIS 47 159 PHE 48 160 ASN 49 161 PRO 50 162 ARG 51 163 PHE 52 164 ASN 53 165 GLU 54 166 ARG 55 167 ASN 56 168 ARG 57 169 ARG 58 170 VAL 59 171 ILE 60 172 VAL 61 173 CYS 62 174 ASN 63 175 THR 64 176 LYS 65 177 LEU 66 178 ASP 67 179 ASN 68 180 ASN 69 181 TRP 70 182 GLY 71 183 ARG 72 184 GLU 73 185 GLU 74 186 ARG 75 187 GLN 76 188 SER 77 189 VAL 78 190 PHE 79 191 PRO 80 192 PHE 81 193 GLU 82 194 SER 83 195 GLY 84 196 LYS 85 197 PRO 86 198 PHE 87 199 LYS 88 200 ILE 89 201 GLN 90 202 VAL 91 203 LEU 92 204 VAL 93 205 GLU 94 206 PRO 95 207 ASP 96 208 HIS 97 209 PHE 98 210 LYS 99 211 VAL 100 212 ALA 101 213 VAL 102 214 ASN 103 215 ASP 104 216 ALA 105 217 HIS 106 218 LEU 107 219 LEU 108 220 GLN 109 221 TYR 110 222 ASN 111 223 HIS 112 224 ARG 113 225 VAL 114 226 LYS 115 227 LYS 116 228 LEU 117 229 ASN 118 230 GLU 119 231 ILE 120 232 SER 121 233 LYS 122 234 LEU 123 235 GLY 124 236 ILE 125 237 SER 126 238 GLY 127 239 ASP 128 240 ILE 129 241 ASP 130 242 LEU 131 243 THR 132 244 SER 133 245 ALA 134 246 SER 135 247 TYR 136 248 THR 137 249 MET 138 250 ILE 139 251 TYR 140 252 ILE 141 253 ASP 142 254 THR 143 255 ASN 144 256 ASN 145 257 ASP 146 258 GLY 147 259 TRP 148 260 TYR 149 261 GLU 150 262 GLY 151 263 ASP 152 264 GLU 153 265 LEU 154 266 LEU 155 267 ALA 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 BMRB 15705 Galectin-3-LBT 100.00 155 100.00 100.00 1.29e-109 BMRB 19491 Galectin-3 88.39 250 99.27 99.27 1.16e-93 BMRB 4909 galectin-3C 88.39 143 99.27 99.27 2.17e-93 PDB 1A3K "X-Ray Crystal Structure Of The Human Galectin-3 Carbohydrate Recognition Domain (Crd) At 2.1 Angstrom Resolution" 88.39 137 99.27 99.27 1.39e-93 PDB 1KJL "High Resolution X-Ray Structure Of Human Galectin-3 In Complex With Lacnac" 88.39 146 99.27 99.27 4.62e-93 PDB 1KJR "Crystal Structure Of The Human Galectin-3 Crd In Complex With A 3'- Derivative Of N-Acetyllactosamine" 88.39 146 99.27 99.27 4.62e-93 PDB 2NMN "Crystal Structure Of Human Galectin-3 Carbohydrate- Recognising Domain At 2.45 Angstrom Resolution" 88.39 138 99.27 99.27 2.10e-93 PDB 2NMO "Crystal Structure Of Human Galectin-3 Carbohydrate-Recognition Domain At 1.35 Angstrom Resolution" 88.39 138 99.27 99.27 2.10e-93 PDB 2NN8 "Crystal Structure Of Human Galectin-3 Carbohydrate-Recognition Domain With Lactose Bound, At 1.35 Angstrom Resolution" 88.39 138 99.27 99.27 2.10e-93 PDB 2XG3 "Human Galectin-3 In Complex With A Benzamido-N- Acetyllactoseamine Inhibitor" 88.39 138 99.27 99.27 1.10e-93 PDB 3AYA "Crystal Structure Of Galectin-3 Crd Domian Complexed With Thomsen- Friedenreich Antigen" 87.10 135 98.52 99.26 7.53e-92 PDB 3AYC "Crystal Structure Of Galectin-3 Crd Domian Complexed With Gm1 Pentasaccharide" 87.10 135 98.52 99.26 7.53e-92 PDB 3AYD "Crystal Structure Of Galectin-3 Crd Domian Complexed With Tfn" 87.10 135 98.52 99.26 7.53e-92 PDB 3AYE "Crystal Structure Of Galectin-3 Crd Domian Complexed With Lactose" 87.10 135 98.52 99.26 7.53e-92 PDB 3T1L "Crystal Structure Of Human Galectin-3 In Complex With Methyl 2-o- Acetyl-3-o-toluoyl-beta-d-talopyranoside" 88.39 143 99.27 99.27 2.17e-93 PDB 3T1M "Crystal Structure Of Human Galectin-3 Carbohydrate Recognition Domain In Complex With Methyl 3-deoxy-2-o-toluoyl-3-n-toluoyl-be" 88.39 143 99.27 99.27 2.17e-93 PDB 3ZSJ "Crystal Structure Of Human Galectin-3 Crd In Complex With Lactose At 0.86 Angstrom Resolution" 88.39 138 99.27 99.27 2.10e-93 PDB 3ZSK "Crystal Structure Of Human Galectin-3 Crd With Glycerol Bound At 0.90 Angstrom Resolution" 89.03 138 99.28 99.28 1.72e-94 PDB 3ZSL "Crystal Structure Of Apo Human Galectin-3 Crd At 1.08 Angstrom Resolution, At Cryogenic Temperature" 89.03 138 99.28 99.28 1.72e-94 PDB 3ZSM "Crystal Structure Of Apo Human Galectin-3 Crd At 1.25 Angstrom Resolution, At Room Temperature" 89.03 138 99.28 99.28 1.72e-94 PDB 4BLI "Galectin-3c In Complex With Bisamido-thiogalactoside Derivate 1" 89.03 138 99.28 99.28 1.72e-94 PDB 4BLJ "Galectin-3c In Complex With Bisamido-thiogalactoside Derivate 2" 89.03 138 99.28 99.28 1.72e-94 PDB 4BM8 "Galectin-3c In Complex With Bisamido-thiogalactoside Derivate 3" 88.39 138 99.27 99.27 1.10e-93 PDB 4JC1 "Galectin-3 Carbohydrate Recognition Domain In Complex With Thiodigalactoside" 88.39 143 99.27 99.27 2.17e-93 PDB 4JCK "Galectin-3 Carbohydrate Recognition Domain In Complex With Thioditaloside" 88.39 143 99.27 99.27 2.17e-93 PDB 4LBJ "Crystal Structure Of Human Galectin-3 Crd K176l Mutant In Complex With Lnt" 89.03 138 98.55 98.55 2.10e-93 PDB 4LBK "Crystal Structure Of Human Galectin-3 Crd K176l Mutant In Complex With Lnnt" 89.03 138 98.55 98.55 2.10e-93 PDB 4LBL "Crystal Structure Of Human Galectin-3 Crd K176l Mutant In Complex With A-gm3" 89.03 138 98.55 98.55 2.10e-93 PDB 4LBM "Crystal Structure Of Human Galectin-3 Crd In Complex With Lnt" 88.39 139 99.27 99.27 2.42e-93 PDB 4LBN "Crystal Structure Of Human Galectin-3 Crd In Complex With Lnnt" 88.39 139 99.27 99.27 2.42e-93 PDB 4LBO "Crystal Structure Of Human Galectin-3 Crd In Complex With A-gm3" 88.39 138 99.27 99.27 2.10e-93 DBJ BAA22164 "galectin-3 [Homo sapiens]" 88.39 250 99.27 99.27 6.09e-94 DBJ BAD92628 "LGALS3 protein variant [Homo sapiens]" 88.39 258 99.27 99.27 2.22e-93 DBJ BAG37435 "unnamed protein product [Homo sapiens]" 88.39 250 99.27 99.27 1.16e-93 DBJ BAI46476 "lectin, galactoside-binding, soluble, 3 [synthetic construct]" 88.39 250 99.27 99.27 6.09e-94 EMBL CAD61918 "unnamed protein product [Homo sapiens]" 78.06 121 99.17 99.17 2.60e-81 EMBL CAG33178 "LGALS3 [Homo sapiens]" 88.39 250 99.27 99.27 6.09e-94 EMBL CAG46894 "LGALS3 [Homo sapiens]" 88.39 250 98.54 98.54 5.32e-93 GB AAA35607 "IgE-binding protein [Homo sapiens]" 88.39 250 99.27 99.27 1.16e-93 GB AAA36163 "laminin-binding protein [Homo sapiens]" 88.39 250 99.27 99.27 1.16e-93 GB AAA88086 "galactose-specific lectin [Homo sapiens]" 88.39 250 99.27 99.27 6.57e-94 GB AAB26229 "carbohydrate binding protein 35 [Homo sapiens]" 88.39 250 99.27 99.27 6.09e-94 GB AAB86584 "galectin 3 [Homo sapiens]" 88.39 250 99.27 99.27 6.09e-94 REF NP_002297 "galectin-3 isoform 1 [Homo sapiens]" 88.39 250 99.27 99.27 6.09e-94 REF XP_001148424 "PREDICTED: galectin-3 [Pan troglodytes]" 88.39 250 97.81 98.54 1.76e-92 REF XP_002824813 "PREDICTED: galectin-3 [Pongo abelii]" 88.39 250 99.27 99.27 7.49e-94 REF XP_003831735 "PREDICTED: galectin-3 [Pan paniscus]" 88.39 250 97.81 98.54 1.40e-92 REF XP_004055252 "PREDICTED: galectin-3 isoform 1 [Gorilla gorilla gorilla]" 88.39 250 98.54 98.54 9.17e-93 SP P17931 "RecName: Full=Galectin-3; Short=Gal-3; AltName: Full=35 kDa lectin; AltName: Full=Carbohydrate-binding protein 35; Short=CBP 35" 88.39 250 99.27 99.27 6.09e-94 stop_ save_ ############# # Ligands # ############# save_LU _Saveframe_category ligand _Mol_type non-polymer _Name_common "LU (LUTETIUM (III) ION)" _BMRB_code . _PDB_code LU _Molecular_mass 174.967 _Mol_charge 3 _Mol_paramagnetic . _Mol_aromatic no _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Fri Feb 15 19:43:54 2008 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons LU LU LU N 3 . ? 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 $Galectin-3-LBT 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 $Galectin-3-LBT 'recombinant technology' . Escherichia coli . pET29-a stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_Diamagnetic_sample _Saveframe_category sample _Sample_type solution _Details '0.3mM LBT-Galectin-3 in 50mM MES/Nacl buffer,pH=5.4 mixing with 0.3mM Lutetium ion' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Galectin-3-LBT 0.3 mM [U-15N] MES 50 mM 'natural abundance' 'sodium chloride' 50 mM 'natural abundance' $LU 0.3 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_VNMRJ _Saveframe_category software _Name VNMRJ _Version . loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task collection stop_ _Details . save_ save_NMRDraw _Saveframe_category software _Name NMRDraw _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task 'peak picking' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-15N_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $Diamagnetic_sample save_ ####################### # Sample conditions # ####################### save_Diamagnetic_condition _Saveframe_category sample_conditions _Details '0.3mM LBT-Galectin-3 in 50mM MES/NaCl pH=5.4 mixing with 0.3mM Lutetium chloride' loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 50 . mM pH 5.4 . pH pressure 1 . atm temperature 298 . 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 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 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_ _Experiment_label '2D 1H-15N HSQC' stop_ loop_ _Sample_label $Diamagnetic_sample stop_ _Sample_conditions_label $Diamagnetic_condition _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name Galectin-3-LBT _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 1 116 4 VAL H H 7.928 . . 2 119 7 ASN H H 7.84 . . 3 139 27 LYS H H 8.306 . . 4 142 30 ALA H H 6.919 . . 5 143 31 ASN H H 9.593 . . 6 144 32 ARG H H 8.6 . . 7 145 33 ILE H H 8.195 . . 8 151 39 ARG H H 8.174 . . 9 154 42 ASP H H 8.485 . . 10 157 45 PHE H H 7.666 . . 11 163 51 PHE H H 8.163 . . 12 164 52 ASN H H 8.726 . . 13 166 54 ARG H H 7.412 . . 14 167 55 ASN H H 8.079 . . 15 172 60 VAL H H 7.355 . . 16 175 63 THR H H 10.072 . . 17 176 64 LYS H H 9.089 . . 18 177 65 LEU H H 7.948 . . 19 179 67 ASN H H 9.184 . . 20 180 68 ASN H H 7.805 . . 21 182 70 GLY H H 8.25 . . 22 185 73 GLU H H 9.181 . . 23 187 75 GLN H H 8.835 . . 24 189 77 VAL H H 7.893 . . 25 227 115 LYS H H 7.112 . . 26 229 117 ASN H H 8.429 . . 27 230 118 GLU H H 7.442 . . 28 232 120 SER H H 7.703 . . 29 233 121 LYS H H 7.891 . . 30 235 123 GLY H H 9.274 . . 31 238 126 GLY H H 8.866 . . 32 240 128 ILE H H 7.902 . . 33 241 129 ASP H H 8.934 . . 34 243 131 THR H H 9.095 . . stop_ save_