data_27039 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Chemical shifts of amorphous-looking aggregates of the P23T mutant of human gamma-D-crystallin formed at pH 7. ; _BMRB_accession_number 27039 _BMRB_flat_file_name bmr27039.str _Entry_type original _Submission_date 2017-02-26 _Accession_date 2017-02-26 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details ; Partial chemical shift assignments of amorphous-looking aggregates of the P23T mutant of human gamma-D-crystallin formed at pH 7. Measurements performed by magic-angle-spinning solid-state NMR. ; loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Boatz Jennifer C. . 2 Whitley Matthew J. . 3 Li Mingyue . . 4 Gronenborn Angela M. . 5 'van der Wel' Patrick C.A. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "13C chemical shifts" 157 "15N chemical shifts" 39 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-05-17 update BMRB 'update entry citation' 2017-05-02 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 16173 'Solution NMR chemical shifts of cataract-causing P23T mutant of HgD crystallin in solution.' stop_ _Original_release_date 2017-02-27 save_ ############################# # Citation for this entry # ############################# save_Citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Cataract-associated P23T gamma-D-crystallin retains a native-like fold in amorphous-looking aggregates formed at physiological pH ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 28474685 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Boatz Jennifer C. . 2 Whitley Matthew J. . 3 Li Mingyue . . 4 Gronenborn Angela M. . 5 'van der Wel' Patrick C.A. . stop_ _Journal_abbreviation 'Nat Commun' _Journal_name_full 'Nature communications' _Journal_volume 8 _Journal_issue . _Journal_ISSN 2041-1723 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 15137 _Page_last 15137 _Year 2017 _Details . loop_ _Keyword 'Magic-angle-spinning NMR' 'Solid-state NMR' stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'P23T HGD aggregated at pH 7' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label gDcrystallinP23T $gD_crystallin_P23T stop_ _System_molecular_weight 20616.9178 _System_physical_state aggregated _System_oligomer_state ? _System_paramagnetic no _System_thiol_state 'all free' loop_ _Biological_function 'Aggregated state formed at neutral pH, with possibly correlations to cataract formation.' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_gD_crystallin_P23T _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common gD_crystallin_P23T _Molecular_mass 20616.9178 _Mol_thiol_state 'all free' loop_ _Biological_function 'Eye lens protein' stop_ _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 173 _Mol_residue_sequence ; GKITLYEDRGFQGRHYECSS DHTNLQPYLSRCNSARVDSG CWMLYEQPNYSGLQYFLRRG DYADHQQWMGLSDSVRSCRL IPHSGSHRIRLYEREDYRGQ MIEFTEDCSCLQDRFRFNEI HSLNVLEGSWVLYELSNYRG RQYLLMPGDYRRYQDWGATN ARVGSLRRVIDFS ; loop_ _Residue_seq_code _Residue_label 1 GLY 2 LYS 3 ILE 4 THR 5 LEU 6 TYR 7 GLU 8 ASP 9 ARG 10 GLY 11 PHE 12 GLN 13 GLY 14 ARG 15 HIS 16 TYR 17 GLU 18 CYS 19 SER 20 SER 21 ASP 22 HIS 23 THR 24 ASN 25 LEU 26 GLN 27 PRO 28 TYR 29 LEU 30 SER 31 ARG 32 CYS 33 ASN 34 SER 35 ALA 36 ARG 37 VAL 38 ASP 39 SER 40 GLY 41 CYS 42 TRP 43 MET 44 LEU 45 TYR 46 GLU 47 GLN 48 PRO 49 ASN 50 TYR 51 SER 52 GLY 53 LEU 54 GLN 55 TYR 56 PHE 57 LEU 58 ARG 59 ARG 60 GLY 61 ASP 62 TYR 63 ALA 64 ASP 65 HIS 66 GLN 67 GLN 68 TRP 69 MET 70 GLY 71 LEU 72 SER 73 ASP 74 SER 75 VAL 76 ARG 77 SER 78 CYS 79 ARG 80 LEU 81 ILE 82 PRO 83 HIS 84 SER 85 GLY 86 SER 87 HIS 88 ARG 89 ILE 90 ARG 91 LEU 92 TYR 93 GLU 94 ARG 95 GLU 96 ASP 97 TYR 98 ARG 99 GLY 100 GLN 101 MET 102 ILE 103 GLU 104 PHE 105 THR 106 GLU 107 ASP 108 CYS 109 SER 110 CYS 111 LEU 112 GLN 113 ASP 114 ARG 115 PHE 116 ARG 117 PHE 118 ASN 119 GLU 120 ILE 121 HIS 122 SER 123 LEU 124 ASN 125 VAL 126 LEU 127 GLU 128 GLY 129 SER 130 TRP 131 VAL 132 LEU 133 TYR 134 GLU 135 LEU 136 SER 137 ASN 138 TYR 139 ARG 140 GLY 141 ARG 142 GLN 143 TYR 144 LEU 145 LEU 146 MET 147 PRO 148 GLY 149 ASP 150 TYR 151 ARG 152 ARG 153 TYR 154 GLN 155 ASP 156 TRP 157 GLY 158 ALA 159 THR 160 ASN 161 ALA 162 ARG 163 VAL 164 GLY 165 SER 166 LEU 167 ARG 168 ARG 169 VAL 170 ILE 171 ASP 172 PHE 173 SER stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . 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 UNP P07320 'Gamma-crystallin D - CRYGD' . . . . . stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Gene_mnemonic $gD_crystallin_P23T Human 9606 Eukaryota Metazoa Homo sapiens CRYGD 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 $gD_crystallin_P23T 'recombinant technology' . Escherichia coli . pET14b stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_gDcrytallinP23T _Saveframe_category sample _Sample_type solid _Details 'Amorphous-looking aggregates (by EM) formed at pH 7' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $gD_crystallin_P23T . mg '[U-99% 13C; U-99% 15N]' stop_ save_ ############################ # Computer software used # ############################ save_CcpNmr_Analysis _Saveframe_category software _Name CcpNmr_Analysis _Version 2.4 loop_ _Vendor _Address _Electronic_address CCPN 'Department of Biochemistry, Cambridge CB2 1GA, UK' http://www.ccpn.ac.uk stop_ loop_ _Task 'chemical shift assignment' stop_ _Details 'The CCPN NMR assignment and data analysis application' save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_3D_NCACX_1 _Saveframe_category NMR_applied_experiment _Experiment_name '3D NCACX' _Sample_label $gDcrytallinP23T save_ save_3D_NCOCX_2 _Saveframe_category NMR_applied_experiment _Experiment_name '3D NCOCX' _Sample_label $gDcrytallinP23T save_ save_2D_DARR_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DARR' _Sample_label $gDcrytallinP23T save_ save_2D_NCACX_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NCACX' _Sample_label $gDcrytallinP23T save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details ; Amorphous-looking aggregates (based on TEM) formed at pH 7 in 100 mM sodium phosphate buffer containing 5 mM dithiothreitol and 0.02% (wt/vol) sodium azide. ; loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7 . 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 C 13 'methyl protons' ppm 0.00 na indirect . . . 0.251449530 DSS N 15 'methyl protons' ppm 0.00 na indirect . . . 0.101329118 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 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $CcpNmr_Analysis stop_ loop_ _Experiment_label '3D NCACX' '3D NCOCX' '2D DARR' '2D NCACX' stop_ loop_ _Sample_label $gDcrytallinP23T stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name gDcrystallinP23T _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 GLY C C 169.5 0.4 1 2 1 1 GLY CA C 43.6 0.4 1 3 2 2 LYS C C 172.9 0.4 1 4 2 2 LYS CA C 57.8 0.4 1 5 2 2 LYS CB C 35.7 0.4 1 6 2 2 LYS CG C 24.6 0.4 1 7 2 2 LYS CD C 26.6 0.4 1 8 2 2 LYS CE C 42.1 0.4 1 9 2 2 LYS N N 124.4 0.5 1 10 3 3 ILE C C 171.5 0.4 1 11 3 3 ILE CA C 58.9 0.4 1 12 3 3 ILE CB C 41.3 0.4 1 13 3 3 ILE CG1 C 28.5 0.4 1 14 3 3 ILE CG2 C 15.3 0.4 1 15 3 3 ILE CD1 C 12.9 0.4 1 16 3 3 ILE N N 128.6 0.5 1 17 4 4 THR C C 172.5 0.4 1 18 4 4 THR CA C 61.8 0.4 1 19 4 4 THR CB C 69.2 0.4 1 20 4 4 THR CG2 C 20.9 0.4 1 21 4 4 THR N N 122.5 0.5 1 22 5 5 LEU C C 175.1 0.4 1 23 5 5 LEU CA C 53.7 0.4 1 24 5 5 LEU CB C 44.1 0.4 1 25 5 5 LEU CG C 27.4 0.4 1 26 5 5 LEU N N 128.2 0.5 1 27 23 23 THR C C 176.4 0.4 1 28 23 23 THR CA C 64.3 0.4 1 29 23 23 THR CB C 72.3 0.4 1 30 23 23 THR CG2 C 22.9 0.4 1 31 23 23 THR N N 113.2 0.5 1 32 26 26 GLN C C 174 0.4 1 33 26 26 GLN CA C 59.5 0.4 1 34 26 26 GLN CB C 28.2 0.4 1 35 26 26 GLN N N 119.5 0.5 1 36 27 27 PRO C C 175.7 0.4 1 37 27 27 PRO CA C 64.6 0.4 1 38 27 27 PRO CB C 30.4 0.4 1 39 27 27 PRO CG C 28 0.4 1 40 27 27 PRO CD C 50.7 0.4 1 41 27 27 PRO N N 130.6 0.5 1 42 34 34 SER C C 173.6 0.4 1 43 34 34 SER CA C 58.8 0.4 1 44 34 34 SER CB C 64.4 0.4 1 45 34 34 SER N N 107.9 0.5 1 46 35 35 ALA C C 175.4 0.4 1 47 35 35 ALA CA C 52.7 0.4 1 48 35 35 ALA CB C 22.8 0.4 1 49 35 35 ALA N N 118.9 0.5 1 50 36 36 ARG C C 175.5 0.4 1 51 36 36 ARG CA C 54.9 0.4 1 52 36 36 ARG CB C 33.9 0.4 1 53 36 36 ARG N N 123.8 0.5 1 54 37 37 VAL C C 175.5 0.4 1 55 37 37 VAL CA C 62.2 0.4 1 56 37 37 VAL CB C 31 0.4 1 57 37 37 VAL CG1 C 23.2 0.4 1 58 37 37 VAL N N 131.8 0.5 1 59 62 62 TYR C C 174.4 0.4 1 60 62 62 TYR CA C 56.3 0.4 1 61 62 62 TYR CB C 39.8 0.4 1 62 62 62 TYR CD1 C 132.2 0.4 3 63 62 62 TYR CD2 C 132.2 0.4 3 64 62 62 TYR N N 122.6 0.5 1 65 63 63 ALA C C 175.7 0.4 1 66 63 63 ALA CA C 53.8 0.4 1 67 63 63 ALA CB C 19.3 0.4 1 68 63 63 ALA N N 126.5 0.5 1 69 80 80 LEU C C 175.7 0.4 1 70 80 80 LEU CA C 53.6 0.4 1 71 80 80 LEU CB C 41.8 0.4 1 72 80 80 LEU CG C 26.8 0.4 1 73 80 80 LEU N N 126 0.5 1 74 81 81 ILE C C 173.8 0.4 1 75 81 81 ILE CA C 60 0.4 1 76 81 81 ILE CB C 42.2 0.4 1 77 81 81 ILE CG1 C 27.7 0.4 1 78 81 81 ILE CG2 C 18.6 0.4 1 79 81 81 ILE N N 130.3 0.5 1 80 82 82 PRO C C 177.1 0.4 1 81 82 82 PRO CA C 63.6 0.4 1 82 82 82 PRO CB C 32.3 0.4 1 83 82 82 PRO CG C 26.4 0.4 1 84 82 82 PRO CD C 51.3 0.4 1 85 82 82 PRO N N 138.1 0.5 1 86 89 89 ILE C C 170.7 0.4 1 87 89 89 ILE CA C 59.1 0.4 1 88 89 89 ILE CB C 42.1 0.4 1 89 89 89 ILE CG1 C 28.1 0.4 1 90 89 89 ILE CG2 C 15.7 0.4 1 91 89 89 ILE CD1 C 14.9 0.4 1 92 89 89 ILE N N 130 0.5 1 93 98 98 ARG C C 175.2 0.4 1 94 98 98 ARG CA C 54.4 0.4 1 95 98 98 ARG CB C 33.1 0.4 1 96 98 98 ARG CG C 27.5 0.4 1 97 98 98 ARG N N 117.7 0.5 1 98 99 99 GLY C C 172.5 0.4 1 99 99 99 GLY CA C 44 0.4 1 100 99 99 GLY N N 105.2 0.5 1 101 100 100 GLN C C 174.2 0.4 1 102 100 100 GLN CA C 57.7 0.4 1 103 100 100 GLN CB C 29.8 0.4 1 104 100 100 GLN CG C 32.6 0.4 1 105 100 100 GLN N N 119.6 0.5 1 106 101 101 MET C C 175.3 0.4 1 107 101 101 MET CA C 53.4 0.4 1 108 101 101 MET CB C 36.1 0.4 1 109 101 101 MET N N 120 0.5 1 110 102 102 ILE C C 171 0.4 1 111 102 102 ILE CA C 60.4 0.4 1 112 102 102 ILE CB C 41.4 0.4 1 113 102 102 ILE CG1 C 28.2 0.4 1 114 102 102 ILE CG2 C 15.5 0.4 1 115 102 102 ILE CD1 C 12.9 0.4 1 116 102 102 ILE N N 124 0.5 1 117 103 103 GLU C C 175.3 0.4 1 118 103 103 GLU CA C 53.7 0.4 1 119 103 103 GLU CB C 33.8 0.4 1 120 103 103 GLU CG C 37.5 0.4 1 121 103 103 GLU CD C 183.6 0.4 1 122 103 103 GLU N N 127.4 0.5 1 123 104 104 PHE C C 176.1 0.4 1 124 104 104 PHE CA C 57.6 0.4 1 125 104 104 PHE CB C 43.5 0.4 1 126 104 104 PHE N N 120.8 0.5 1 127 105 105 THR C C 173.3 0.4 1 128 105 105 THR CA C 61 0.4 1 129 105 105 THR CB C 70.5 0.4 1 130 105 105 THR CG2 C 21.5 0.4 1 131 105 105 THR N N 108.8 0.5 1 132 107 107 ASP C C 176.4 0.4 1 133 107 107 ASP CA C 55.5 0.4 1 134 107 107 ASP CB C 41.4 0.4 1 135 107 107 ASP N N 115.8 0.5 1 136 108 108 CYS C C 174.2 0.4 1 137 108 108 CYS CA C 57.8 0.4 1 138 108 108 CYS CB C 28.7 0.4 1 139 108 108 CYS N N 121.3 0.5 1 140 109 109 SER C C 173.9 0.4 1 141 109 109 SER CA C 60.9 0.4 1 142 109 109 SER CB C 62.8 0.4 1 143 109 109 SER N N 124.5 0.5 1 144 120 120 ILE C C 173.9 0.4 1 145 120 120 ILE CA C 57.9 0.4 1 146 120 120 ILE CB C 38.7 0.4 1 147 120 120 ILE CG1 C 26.9 0.4 1 148 120 120 ILE CG2 C 19.4 0.4 1 149 120 120 ILE CD1 C 11.5 0.4 1 150 120 120 ILE N N 122.7 0.5 1 151 156 156 TRP C C 176.6 0.4 1 152 156 156 TRP CA C 57.1 0.4 1 153 156 156 TRP CB C 28.2 0.4 1 154 156 156 TRP N N 114.9 0.5 1 155 157 157 GLY C C 173.4 0.4 1 156 157 157 GLY CA C 46.1 0.4 1 157 157 157 GLY N N 108 0.5 1 158 158 158 ALA C C 177 0.4 1 159 158 158 ALA CA C 51.4 0.4 1 160 158 158 ALA CB C 22.2 0.4 1 161 158 158 ALA N N 120 0.5 1 162 159 159 THR C C 175.4 0.4 1 163 159 159 THR CA C 61.3 0.4 1 164 159 159 THR CB C 70.7 0.4 1 165 159 159 THR CG2 C 22.2 0.4 1 166 159 159 THR N N 106.3 0.5 1 167 160 160 ASN C C 171.7 0.4 1 168 160 160 ASN CA C 52.1 0.4 1 169 160 160 ASN CB C 39.5 0.4 1 170 160 160 ASN CG C 176.5 0.4 1 171 160 160 ASN N N 117.2 0.5 1 172 161 161 ALA C C 176.4 0.4 1 173 161 161 ALA CA C 51.4 0.4 1 174 161 161 ALA CB C 19.3 0.4 1 175 161 161 ALA N N 119.6 0.5 1 176 162 162 ARG C C 176.9 0.4 1 177 162 162 ARG CA C 58.6 0.4 1 178 162 162 ARG CB C 29.6 0.4 1 179 162 162 ARG N N 119.8 0.5 1 180 163 163 VAL C C 174.4 0.4 1 181 163 163 VAL CA C 61.7 0.4 1 182 163 163 VAL CB C 36.4 0.4 1 183 163 163 VAL N N 120.7 0.5 1 184 169 169 VAL C C 174.7 0.4 1 185 169 169 VAL CA C 65.2 0.4 1 186 169 169 VAL CB C 30 0.4 1 187 169 169 VAL CG1 C 20.7 0.4 1 188 169 169 VAL CG2 C 21.8 0.4 1 189 169 169 VAL N N 124.3 0.5 1 190 170 170 ILE C C 173.9 0.4 1 191 170 170 ILE CA C 58.1 0.4 1 192 170 170 ILE CB C 40.4 0.4 1 193 170 170 ILE CG1 C 25.3 0.4 1 194 170 170 ILE CG2 C 20.2 0.4 1 195 170 170 ILE CD1 C 17 0.4 1 196 170 170 ILE N N 130.1 0.5 1 stop_ save_