data_17356 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Biophysical studies of lipid interacting regions of DGD2 in Arabidopsis thaliana ; _BMRB_accession_number 17356 _BMRB_flat_file_name bmr17356.str _Entry_type original _Submission_date 2010-12-10 _Accession_date 2010-12-10 _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 Szpryngiel Scarlett . . 2 Ge Changrong . . 3 Iakovleva Irina . . 4 Lind Jesper . . 5 Wieslander Ake . . 6 Maler Lena . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 98 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2011-05-27 update author 'update entry citation' 2011-05-05 original author 'original release' stop_ _Original_release_date 2010-12-10 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Lipid Interacting Regions in Phosphate Stress Glycosyltransferase atDGD2 from Arabidopsis thaliana. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 21506606 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Szpryngiel Scarlett . . 2 Ge Changrong . . 3 Iakovleva Irina . . 4 Georgiev Alexander . . 5 Lind Jesper . . 6 Wieslander Ake . . 7 Maler Lena . . stop_ _Journal_abbreviation Biochemistry _Journal_name_full Biochemistry _Journal_volume 50 _Journal_issue 21 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 4451 _Page_last 4466 _Year 2011 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name DGD2 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label DGD2 $atDGD2_S227_245 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_atDGD2_S227_245 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common atDGD2_S227_245 _Molecular_mass 2227.622 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 19 _Mol_residue_sequence ; QPFTKGAYYIGKMVWSKGY ; loop_ _Residue_seq_code _Residue_label 1 GLN 2 PRO 3 PHE 4 THR 5 LYS 6 GLY 7 ALA 8 TYR 9 TYR 10 ILE 11 GLY 12 LYS 13 MET 14 VAL 15 TRP 16 SER 17 LYS 18 GLY 19 TYR stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $atDGD2_S227_245 'thale cress' 3702 Eukaryota Viridiplantae Arabidopsis thaliana 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 $atDGD2_S227_245 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type micelle _Details '50 mM DPC-d38' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $atDGD2_S227_245 0.5 mM 'natural abundance' DPC 50 mM [U-2H] D2O 10 % [U-2H] 'sodium phosphate' 50 mM 'natural abundance' H2O 90 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CYANA _Saveframe_category software _Name CYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' 'peak picking' stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 500 _Details 'with cryo probe' save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 50 . mM pH 5.7 . pH pressure 1 . atm temperature 273 . 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 water H 1 protons ppm 4.705 internal direct . . . 1 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-1H TOCSY' '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name DGD2 _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 GLN H H 8.365 0.02 1 2 1 1 GLN HA H 4.327 0.02 1 3 1 1 GLN HB2 H 1.834 0.02 2 4 1 1 GLN HB3 H 1.867 0.02 2 5 1 1 GLN HG2 H 2.221 0.02 2 6 1 1 GLN HE21 H 7.482 0.02 2 7 1 1 GLN HE22 H 6.651 0.02 2 8 2 2 PRO HA H 4.176 0.02 1 9 2 2 PRO HB2 H 2.043 0.02 2 10 2 2 PRO HD2 H 3.558 0.02 2 11 3 3 PHE H H 8.26 0.02 1 12 3 3 PHE HA H 4.229 0.02 1 13 3 3 PHE HB2 H 2.989 0.02 2 14 3 3 PHE HB3 H 3 0.02 2 15 3 3 PHE HD1 H 7.066 0.02 3 16 3 3 PHE HE1 H 7.084 0.02 3 17 3 3 PHE HZ H 7.05 0.02 1 18 4 4 THR H H 7.846 0.02 1 19 4 4 THR HA H 4.035 0.02 1 20 4 4 THR HB H 3.714 0.02 1 21 4 4 THR HG2 H 1.045 0.02 1 22 5 5 LYS H H 7.811 0.02 1 23 5 5 LYS HA H 3.924 0.02 1 24 5 5 LYS HB2 H 1.652 0.02 2 25 5 5 LYS HD2 H 1.508 0.02 3 26 5 5 LYS HD3 H 1.453 0.02 3 27 6 6 GLY H H 8.162 0.02 1 28 6 6 GLY HA2 H 3.643 0.02 2 29 6 6 GLY HA3 H 3.75 0.02 2 30 7 7 ALA H H 8.254 0.02 1 31 7 7 ALA HA H 3.805 0.02 1 32 7 7 ALA HB H 1.22 0.02 1 33 8 8 TYR H H 8.073 0.02 1 34 8 8 TYR HA H 3.922 0.02 1 35 8 8 TYR HB2 H 2.909 0.02 2 36 8 8 TYR HB3 H 3.008 0.02 2 37 8 8 TYR HD1 H 6.932 0.02 3 38 8 8 TYR HE1 H 6.733 0.02 3 39 9 9 TYR H H 7.787 0.02 1 40 9 9 TYR HA H 3.864 0.02 1 41 9 9 TYR HB2 H 3.008 0.02 2 42 9 9 TYR HB3 H 2.908 0.02 2 43 9 9 TYR HD1 H 6.94 0.02 3 44 9 9 TYR HE1 H 6.731 0.02 3 45 10 10 ILE H H 7.978 0.02 1 46 10 10 ILE HA H 3.495 0.02 1 47 10 10 ILE HB H 1.827 0.02 1 48 10 10 ILE HG12 H 1.495 0.02 2 49 10 10 ILE HG13 H 1.267 0.02 2 50 10 10 ILE HG2 H 0.841 0.02 1 51 10 10 ILE HD1 H 0.696 0.02 1 52 11 11 GLY H H 8.491 0.02 1 53 11 11 GLY HA2 H 3.444 0.02 2 54 12 12 LYS H H 8.204 0.02 1 55 12 12 LYS HA H 3.742 0.02 1 56 12 12 LYS HB2 H 1.584 0.02 2 57 12 12 LYS HG2 H 1.137 0.02 2 58 12 12 LYS HE2 H 2.677 0.02 2 59 13 13 MET H H 7.614 0.02 1 60 13 13 MET HA H 3.996 0.02 1 61 13 13 MET HB2 H 1.87 0.02 2 62 13 13 MET HB3 H 2 0.02 2 63 13 13 MET HG2 H 2.306 0.02 2 64 14 14 VAL H H 8.093 0.02 1 65 14 14 VAL HA H 3.468 0.02 1 66 14 14 VAL HB H 2.022 0.02 1 67 14 14 VAL HG1 H 0.8 0.02 2 68 14 14 VAL HG2 H 0.755 0.02 2 69 15 15 TRP H H 8.355 0.02 1 70 15 15 TRP HA H 4.13 0.02 1 71 15 15 TRP HB2 H 3.161 0.02 2 72 15 15 TRP HB3 H 3.135 0.02 2 73 15 15 TRP HD1 H 6.972 0.02 1 74 15 15 TRP HE1 H 10.279 0.02 1 75 15 15 TRP HE3 H 7.391 0.02 1 76 15 15 TRP HZ2 H 7.4 0.02 1 77 15 15 TRP HZ3 H 6.917 0.02 1 78 15 15 TRP HH2 H 7.003 0.02 1 79 16 16 SER H H 7.979 0.02 1 80 16 16 SER HA H 3.937 0.02 1 81 16 16 SER HB2 H 3.793 0.02 2 82 16 16 SER HB3 H 3.818 0.02 2 83 17 17 LYS H H 7.63 0.02 1 84 17 17 LYS HA H 4.014 0.02 1 85 17 17 LYS HB2 H 1.666 0.02 2 86 17 17 LYS HB3 H 1.597 0.02 2 87 17 17 LYS HG2 H 1.29 0.02 3 88 17 17 LYS HD2 H 1.465 0.02 3 89 17 17 LYS HD3 H 1.415 0.02 3 90 17 17 LYS HZ H 7.102 0.02 1 91 18 18 GLY H H 7.833 0.02 1 92 18 18 GLY HA2 H 3.515 0.02 2 93 19 19 TYR H H 7.635 0.02 1 94 19 19 TYR HA H 4.122 0.02 1 95 19 19 TYR HB2 H 2.577 0.02 2 96 19 19 TYR HB3 H 2.329 0.02 2 97 19 19 TYR HD1 H 7.106 0.02 3 98 19 19 TYR HE1 H 6.711 0.02 3 stop_ save_