data_25394 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; complex structure of Dvl PDZ domain with ligand ; _BMRB_accession_number 25394 _BMRB_flat_file_name bmr25394.str _Entry_type original _Submission_date 2015-12-28 _Accession_date 2015-12-28 _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 Zhang Xinxin . . 2 Zheng Jie J. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 39 "13C chemical shifts" 24 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2015-12-28 original BMRB . stop_ _Original_release_date 2015-12-28 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Protein-ligand interaction decoded by NMR chemical shift analysis ; _Citation_status 'in preparation' _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Zhang Xinxin . . 2 Zheng Jie J. . stop_ _Journal_abbreviation 'Not known' _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'complex of Dvl PDZ domain with ligand' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity_1 entity_2 $entity_2 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_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity_1 _Molecular_mass 9632.958 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 90 _Mol_residue_sequence ; NIITVTLNMERHHFLGISIV GQSNDRGDGGIYIGSIMKGG AVAADGRIEPGDMLLQVNDV NFENMSNDDAVRVLREIVSQ TGPISLTVAK ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 248 ASN 2 249 ILE 3 250 ILE 4 251 THR 5 252 VAL 6 253 THR 7 254 LEU 8 255 ASN 9 256 MET 10 257 GLU 11 258 ARG 12 259 HIS 13 260 HIS 14 261 PHE 15 262 LEU 16 263 GLY 17 264 ILE 18 265 SER 19 266 ILE 20 267 VAL 21 268 GLY 22 269 GLN 23 270 SER 24 271 ASN 25 272 ASP 26 273 ARG 27 274 GLY 28 275 ASP 29 276 GLY 30 277 GLY 31 278 ILE 32 279 TYR 33 280 ILE 34 281 GLY 35 282 SER 36 283 ILE 37 284 MET 38 285 LYS 39 286 GLY 40 287 GLY 41 288 ALA 42 289 VAL 43 290 ALA 44 291 ALA 45 292 ASP 46 293 GLY 47 294 ARG 48 295 ILE 49 296 GLU 50 297 PRO 51 298 GLY 52 299 ASP 53 300 MET 54 301 LEU 55 302 LEU 56 303 GLN 57 304 VAL 58 305 ASN 59 306 ASP 60 307 VAL 61 308 ASN 62 309 PHE 63 310 GLU 64 311 ASN 65 312 MET 66 313 SER 67 314 ASN 68 315 ASP 69 316 ASP 70 317 ALA 71 318 VAL 72 319 ARG 73 320 VAL 74 321 LEU 75 322 ARG 76 323 GLU 77 324 ILE 78 325 VAL 79 326 SER 80 327 GLN 81 328 THR 82 329 GLY 83 330 PRO 84 331 ILE 85 332 SER 86 333 LEU 87 334 THR 88 335 VAL 89 336 ALA 90 337 LYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_entity_2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity_2 _Molecular_mass 303.360 _Mol_thiol_state 'not present' _Details . _Residue_count 3 _Mol_residue_sequence ; XWV ; loop_ _Residue_seq_code _Residue_label 1 PHQ 2 TRP 3 VAL stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_PHQ _Saveframe_category polymer_residue _Mol_type NON-POLYMER _Name_common 'benzyl chlorocarbonate' _BMRB_code PHQ _PDB_code PHQ _Standard_residue_derivative . _Molecular_mass 170.593 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C1 C1 C . 0 . ? O1 O1 O . 0 . ? O2 O2 O . 0 . ? C2 C2 C . 0 . ? C3 C3 C . 0 . ? C4 C4 C . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? C7 C7 C . 0 . ? C8 C8 C . 0 . ? CL1 CL1 CL . 0 . ? H21 H21 H . 0 . ? H22 H22 H . 0 . ? H41 H41 H . 0 . ? H51 H51 H . 0 . ? H61 H61 H . 0 . ? H71 H71 H . 0 . ? H81 H81 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 C1 O1 ? ? SING C1 O2 ? ? SING C1 CL1 ? ? SING O2 C2 ? ? SING C2 C3 ? ? SING C2 H21 ? ? SING C2 H22 ? ? DOUB C3 C4 ? ? SING C3 C8 ? ? SING C4 C5 ? ? SING C4 H41 ? ? DOUB C5 C6 ? ? SING C5 H51 ? ? SING C6 C7 ? ? SING C6 H61 ? ? DOUB C7 C8 ? ? SING C7 H71 ? ? SING C8 H81 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity_1 Mouse 10090 Eukaryota Metazoa . . $entity_2 . . . . . . 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 $entity_1 'recombinant technology' . . . . pET28a $entity_2 'obtained from a vendor' . . . . . 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 $entity_1 1 mM '[U-100% 13C; U-100% 15N]' $entity_2 10 mM 'natural abundance' 'potassium phosphate' 100 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CNS _Saveframe_category software _Name CNS _Version . loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_Bruker _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_3D_1H-13C_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-13C NOESY' _Sample_label $sample_1 save_ save_2D_1H-15N_HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_3D_HNCA_3 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCA' _Sample_label $sample_1 save_ save_3D_HNCACB_4 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCACB' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _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' 0.1 . M pH 7.5 . 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 internal indirect . . . 0.25144953 DSS H 1 'methyl protons' ppm 0 internal direct . . . 1 DSS N 15 'methyl protons' ppm 0 internal indirect . . . 0.10132905 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_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '3D 1H-13C 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 entity_2 _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 PHQ HB2 H 4.78578 0.0 2 2 1 1 PHQ HD1 H 7.107115 0.0 3 3 1 1 PHQ HE1 H 7.136735 0.0 3 4 2 2 TRP H H 6.98018 0.0 1 5 2 2 TRP HA H 4.35909 0.0 1 6 2 2 TRP HB2 H 3.150195 0.0 2 7 2 2 TRP HD1 H 7.18582 0.0 1 8 2 2 TRP HE3 H 7.45886 0.0 1 9 2 2 TRP HZ2 H 7.31395 0.0 1 10 2 2 TRP HZ3 H 7.03466 0.0 1 11 2 2 TRP HH2 H 6.9638975 0.0 1 12 3 3 VAL H H 7.4241 0.0 1 13 3 3 VAL HB H 1.87134666667 0.0 1 14 3 3 VAL HG1 H 0.659175 0.0 2 15 3 3 VAL HG2 H 0.873865185185 0.0 2 stop_ save_ save_assigned_chem_shift_list_1_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '3D 1H-13C 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 entity_1 _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 1 256 9 MET HE H 1.60284 0.0 1 2 256 9 MET CE C 12.43449 0.0 1 3 262 15 LEU HB2 H 1.38502 0.0 2 4 262 15 LEU CB C 39.4291 0.0 1 5 264 17 ILE HD1 H 0.40567 0.0 1 6 264 17 ILE CD1 C 10.03581 0.0 1 7 266 19 ILE HG12 H 1.28878 0.0 2 8 266 19 ILE HG2 H 0.50312 0.0 1 9 266 19 ILE HD1 H 0.3450075 0.0 1 10 266 19 ILE CG1 C 20.0145033333 0.0 1 11 266 19 ILE CG2 C 15.65883 0.0 1 12 266 19 ILE CD1 C 9.0716675 0.0 1 13 278 31 ILE HG2 H 0.51146 0.0 1 14 278 31 ILE CG2 C 16.628805 0.0 1 15 284 37 MET HB2 H 1.68980666667 0.0 2 16 284 37 MET HE H 1.167791 0.0 1 17 284 37 MET CB C 32.2002333333 0.0 1 18 284 37 MET CE C 13.838176 0.0 1 19 289 42 VAL HA H 3.26384 0.0 1 20 289 42 VAL HB H 1.81024 0.0 1 21 289 42 VAL CA C 24.08885 0.0 1 22 289 42 VAL CB C 28.93541 0.0 1 23 290 43 ALA HB H 1.29119 0.0 1 24 290 43 ALA CB C 15.97122 0.0 1 25 317 70 ALA HB H 1.083985 0.0 1 26 317 70 ALA CB C 16.28361 0.0 1 27 318 71 VAL HB H 2.05147 0.0 1 28 318 71 VAL HG1 H 0.98104 0.0 2 29 318 71 VAL HG2 H 0.99332 0.0 2 30 318 71 VAL CB C 28.72048 0.0 1 31 318 71 VAL CG1 C 19.41168 0.0 2 32 318 71 VAL CG2 C 20.965475 0.0 2 33 321 74 LEU HB2 H 1.10885 0.0 2 34 321 74 LEU HG H 1.67262 0.0 1 35 321 74 LEU CB C 38.842735 0.0 1 36 321 74 LEU CG C 30.96595 0.0 1 37 322 75 ARG HB2 H 1.77513 0.0 2 38 322 75 ARG HG2 H 1.66033 0.0 2 39 322 75 ARG HD2 H 2.77295 0.0 2 40 322 75 ARG CB C 27.209345 0.0 1 41 322 75 ARG CG C 24.791605 0.0 1 42 322 75 ARG CD C 40.998685 0.0 1 43 324 77 ILE HB H 1.61825 0.0 1 44 324 77 ILE CB C 35.808 0.0 1 45 325 78 VAL HB H 15.443985 0.0 1 46 325 78 VAL HG2 H 1.11029 0.0 2 47 325 78 VAL CB C 15.597025 0.0 1 48 325 78 VAL CG2 C 19.25132 0.0 2 stop_ save_