data_4124 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Main-chain Signal Assignment for the PDZ2 Domain from Human Protein Tyrosine Phosphatase hPTP1E and its Complex with a C-terminal Peptide from the Fas Receptor ; _BMRB_accession_number 4124 _BMRB_flat_file_name bmr4124.str _Entry_type original _Submission_date 1998-03-17 _Accession_date 1998-03-17 _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 Ekiel Irena . . 2 Banville Denis . . 3 Shen 'Shi Hsiang' . . 4 Slon-Usakiewicz Jacek J . 5 Koshy Alex . . 6 Gehring Kalle . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 88 "15N chemical shifts" 88 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 1999-02-02 original author . stop_ _Original_release_date 1999-02-02 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full ; Ekiel, I., Banville, D., Shen, S. H., Slon-Usakiewicz, J. J., Koshy, A., Gehring, K., "Main-chain Signal Assignment for the PDZ2 Domain from Human Protein Tyrosine Phosphatase hPTP1E and its Complex with a C-terminal Peptide from the Fas Receptor," J. Biomol. NMR 12, 455-456 (1998). ; _Citation_title ; Main-chain Signal Assignment for the PDZ2Domain from Human Protein Tyrosine Phosphatase hPTP1E and its Complex with a C-terminal Peptide from the Fas Receptor ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 99052117 _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Ekiel Irena . . 2 Banville Denis . . 3 Shen 'Shi Hsiang' . . 4 Slon-Usakiewicz Jacek J . 5 Koshy Alex . . 6 Gehring Kalle . . stop_ _Journal_abbreviation 'J. Biomol. NMR' _Journal_volume 12 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 455 _Page_last 456 _Year 1998 _Details . loop_ _Keyword hPTP1E PDZ PTPbas PTPL1Fas stop_ save_ ####################################### # Cited references within the entry # ####################################### save_citation_one _Saveframe_category citation _Citation_full ; Wishart, D. S., Bigam, C. G., Yao, J., Abildgaard, F., Dyson, J. H., Oldfield, E., Markley, J. L., and Sykes, B. D., J. Biomol. NMR 6, 135-140 (1995). ; _Citation_title '1H, 13C and 15N chemical shift referencing in biomolecular NMR.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 8589602 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Wishart 'D S' S. . 2 Bigam 'C G' G. . 3 Yao J . . 4 Abildgaard F . . 5 Dyson 'H J' J. . 6 Oldfield E . . 7 Markley 'J L' L. . 8 Sykes 'B D' D. . stop_ _Journal_abbreviation 'J. Biomol. NMR' _Journal_name_full 'Journal of biomolecular NMR' _Journal_volume 6 _Journal_issue 2 _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first 135 _Page_last 140 _Year 1995 _Details ; A considerable degree of variability exists in the way that 1H, 13C and 15N chemical shifts are reported and referenced for biomolecules. In this article we explore some of the reasons for this situation and propose guidelines for future chemical shift referencing and for conversion from many common 1H, 13C and 15N chemical shift standards, now used in biomolecular NMR, to those proposed here. ; save_ ################################## # Molecular system description # ################################## save_system_PDZ2_Fas_complex _Saveframe_category molecular_system _Mol_system_name 'hPTP1E-Fas receptor complex' _Abbreviation_common PDZ2 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label PDZ2 $PDZ2 Fas_Cterm15 $Fas_Cterm15 stop_ _System_molecular_weight 11758 _System_physical_state native _System_oligomer_state hetero-dimer _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_PDZ2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'second PDZ domain from hPTP1E' _Abbreviation_common PDZ2 _Molecular_mass 10006 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 96 _Mol_residue_sequence ; PKPGDIFEVELAKNDNSLGI SVTGGVNTSVRHGGIYVKAV IPQGAAESDGRIHKGDRVLA VNGVSLEGATHKQAVETLRN TGQVVHLLLEKGQSPT ; loop_ _Residue_seq_code _Residue_label 1 PRO 2 LYS 3 PRO 4 GLY 5 ASP 6 ILE 7 PHE 8 GLU 9 VAL 10 GLU 11 LEU 12 ALA 13 LYS 14 ASN 15 ASP 16 ASN 17 SER 18 LEU 19 GLY 20 ILE 21 SER 22 VAL 23 THR 24 GLY 25 GLY 26 VAL 27 ASN 28 THR 29 SER 30 VAL 31 ARG 32 HIS 33 GLY 34 GLY 35 ILE 36 TYR 37 VAL 38 LYS 39 ALA 40 VAL 41 ILE 42 PRO 43 GLN 44 GLY 45 ALA 46 ALA 47 GLU 48 SER 49 ASP 50 GLY 51 ARG 52 ILE 53 HIS 54 LYS 55 GLY 56 ASP 57 ARG 58 VAL 59 LEU 60 ALA 61 VAL 62 ASN 63 GLY 64 VAL 65 SER 66 LEU 67 GLU 68 GLY 69 ALA 70 THR 71 HIS 72 LYS 73 GLN 74 ALA 75 VAL 76 GLU 77 THR 78 LEU 79 ARG 80 ASN 81 THR 82 GLY 83 GLN 84 VAL 85 VAL 86 HIS 87 LEU 88 LEU 89 LEU 90 GLU 91 LYS 92 GLY 93 GLN 94 SER 95 PRO 96 THR stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-02-04 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 18833 PDZ 100.00 97 97.92 97.92 6.64e-59 BMRB 18834 PDZ 100.00 97 97.92 97.92 6.64e-59 BMRB 4123 "second PDZ domain from human phosphatase hPTP1E" 100.00 96 100.00 100.00 1.34e-60 BMRB 4516 "HUMAN PHOSPHATASE HPTP1E" 100.00 96 100.00 100.00 1.34e-60 PDB 1D5G "Solution Structure Of The Pdz2 Domain From Human Phosphatase Hptp1e Complexed With A Peptide" 98.96 96 100.00 100.00 1.53e-59 PDB 2M0Z "Cis Form Of A Photoswitchable Pdz Domain Crosslinked With An Azobenzene Derivative" 100.00 97 97.92 97.92 6.64e-59 PDB 2M10 "Trans Form Of A Photoswitchable Pdz Domain Crosslinked With An Azobenzene Derivative" 100.00 97 97.92 97.92 6.64e-59 PDB 3LNX "Second Pdz Domain From Human Ptp1e" 100.00 96 100.00 100.00 1.34e-60 PDB 3LNY "Second Pdz Domain From Human Ptp1e In Complex With Ra-Gef2 Peptide" 100.00 96 100.00 100.00 1.34e-60 PDB 3PDZ "Solution Structure Of The Pdz2 Domain From Human Phosphatase Hptp1e" 100.00 96 100.00 100.00 1.34e-60 stop_ save_ save_Fas_Cterm15 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'C-terminal peptide from the Fas receptor' _Abbreviation_common Fas_Cterm15 _Molecular_mass 1752 _Mol_thiol_state . _Details . _Residue_count 15 _Mol_residue_sequence DSENSNFRNEIQSLV loop_ _Residue_seq_code _Residue_label 1 ASP 2 SER 3 GLU 4 ASN 5 SER 6 ASN 7 PHE 8 ARG 9 ASN 10 GLU 11 ILE 12 GLN 13 SER 14 LEU 15 VAL stop_ _Sequence_homology_query_date 2008-08-19 _Sequence_homology_query_revised_last_date 2008-08-19 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 EMBL CAD48931 'CD95 antigen [Homo sapiens]' 100.00 109 100.00 100.00 8.96e+00 EMBL CAD48932 'CD95 antigen [Homo sapiens]' 100.00 109 100.00 100.00 9.04e+00 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $PDZ2 Human 9606 Eukaryota Metazoa Homo sapiens $Fas_Cterm15 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 $PDZ2 'recombinant technology' 'E. coli' Escherichia coli . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_one _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $system_PDZ2_Fas_complex 3 mM '[U-15N; U-13C]' 'sodium phosphate buffer' 50 mM . 'sodium chloride' 150 mM . H2O 90 % . D2O 10 % . stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_one _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX500 _Field_strength 500 _Details . save_ ####################### # Sample conditions # ####################### save_sample_conditions_one _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.9 0.1 n/a pressure 1 . atm temperature 293 1 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_one _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 0.0 . indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0.0 internal direct . . . . DSS N 15 'methyl protons' ppm 0.0 . 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_chemical_shift_assignment_one _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_one stop_ _Sample_conditions_label $sample_conditions_one _Chem_shift_reference_set_label $chemical_shift_reference_one _Mol_system_component_name PDZ2 _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 . 2 LYS H H 9.07 0.01 1 2 . 2 LYS N N 123.8 0.1 1 3 . 4 GLY H H 8.99 0.01 1 4 . 4 GLY N N 113.5 0.1 1 5 . 5 ASP H H 8.38 0.01 1 6 . 5 ASP N N 122.0 0.1 1 7 . 6 ILE H H 8.34 0.01 1 8 . 6 ILE N N 121.7 0.1 1 9 . 7 PHE H H 9.46 0.01 1 10 . 7 PHE N N 126.4 0.1 1 11 . 8 GLU H H 8.52 0.01 1 12 . 8 GLU N N 119.3 0.1 1 13 . 9 VAL H H 8.52 0.01 1 14 . 9 VAL N N 116.2 0.1 1 15 . 10 GLU H H 7.68 0.01 1 16 . 10 GLU N N 126.4 0.1 1 17 . 11 LEU H H 8.78 0.01 1 18 . 11 LEU N N 126.1 0.1 1 19 . 12 ALA H H 8.45 0.01 1 20 . 12 ALA N N 126.4 0.1 1 21 . 13 LYS H H 8.56 0.01 1 22 . 13 LYS N N 120.2 0.1 1 23 . 14 ASN H H 8.05 0.01 1 24 . 14 ASN N N 117.3 0.1 1 25 . 15 ASP H H 9.30 0.01 1 26 . 15 ASP N N 127.0 0.1 1 27 . 16 ASN H H 9.04 0.01 1 28 . 16 ASN N N 110.1 0.1 1 29 . 17 SER H H 7.85 0.01 1 30 . 17 SER N N 112.9 0.1 1 31 . 19 GLY H H 9.24 0.01 1 32 . 19 GLY N N 107.9 0.1 1 33 . 20 ILE H H 7.89 0.01 1 34 . 20 ILE N N 117.1 0.1 1 35 . 21 SER H H 8.65 0.01 1 36 . 21 SER N N 117.9 0.1 1 37 . 22 VAL H H 9.28 0.01 1 38 . 22 VAL N N 118.6 0.1 1 39 . 23 THR H H 9.18 0.01 1 40 . 23 THR N N 115.4 0.1 1 41 . 24 GLY H H 8.84 0.01 1 42 . 24 GLY N N 111.4 0.1 1 43 . 26 VAL H H 8.46 0.01 1 44 . 26 VAL N N 117.0 0.1 1 45 . 27 ASN H H 9.09 0.01 1 46 . 27 ASN N N 116.4 0.1 1 47 . 28 THR H H 7.65 0.01 1 48 . 28 THR N N 111.4 0.1 1 49 . 29 SER H H 8.61 0.01 1 50 . 29 SER N N 113.6 0.1 1 51 . 30 VAL H H 7.51 0.01 1 52 . 30 VAL N N 118.2 0.1 1 53 . 31 ARG H H 8.60 0.01 1 54 . 31 ARG N N 125.7 0.1 1 55 . 33 GLY H H 8.50 0.01 1 56 . 33 GLY N N 108.9 0.1 1 57 . 34 GLY H H 7.64 0.01 1 58 . 34 GLY N N 104.6 0.1 1 59 . 35 ILE H H 8.35 0.01 1 60 . 35 ILE N N 118.9 0.1 1 61 . 36 TYR H H 9.04 0.01 1 62 . 36 TYR N N 123.6 0.1 1 63 . 37 VAL H H 9.11 0.01 1 64 . 37 VAL N N 120.4 0.1 1 65 . 38 LYS H H 9.59 0.01 1 66 . 38 LYS N N 135.4 0.1 1 67 . 39 ALA H H 7.61 0.01 1 68 . 39 ALA N N 117.3 0.1 1 69 . 40 VAL H H 8.78 0.01 1 70 . 40 VAL N N 121.4 0.1 1 71 . 41 ILE H H 7.80 0.01 1 72 . 41 ILE N N 128.9 0.1 1 73 . 43 GLN H H 9.35 0.01 1 74 . 43 GLN N N 117.1 0.1 1 75 . 44 GLY H H 7.76 0.01 1 76 . 44 GLY N N 106.4 0.1 1 77 . 45 ALA H H 9.11 0.01 1 78 . 45 ALA N N 121.7 0.1 1 79 . 46 ALA H H 8.01 0.01 1 80 . 46 ALA N N 119.7 0.1 1 81 . 47 GLU H H 9.50 0.01 1 82 . 47 GLU N N 124.8 0.1 1 83 . 48 SER H H 8.03 0.01 1 84 . 48 SER N N 113.9 0.1 1 85 . 49 ASP H H 7.62 0.01 1 86 . 49 ASP N N 120.1 0.1 1 87 . 50 GLY H H 7.33 0.01 1 88 . 50 GLY N N 103.2 0.1 1 89 . 51 ARG H H 7.88 0.01 1 90 . 51 ARG N N 117.6 0.1 1 91 . 52 ILE H H 8.31 0.01 1 92 . 52 ILE N N 120.7 0.1 1 93 . 53 HIS H H 9.09 0.01 1 94 . 53 HIS N N 123.5 0.1 1 95 . 54 LYS H H 8.66 0.01 1 96 . 54 LYS N N 120.8 0.1 1 97 . 55 GLY H H 9.35 0.01 1 98 . 55 GLY N N 115.1 0.1 1 99 . 56 ASP H H 8.07 0.01 1 100 . 56 ASP N N 122.3 0.1 1 101 . 57 ARG H H 8.98 0.01 1 102 . 57 ARG N N 122.9 0.1 1 103 . 58 VAL H H 8.93 0.01 1 104 . 58 VAL N N 126.4 0.1 1 105 . 59 LEU H H 9.24 0.01 1 106 . 59 LEU N N 127.3 0.1 1 107 . 60 ALA H H 7.69 0.01 1 108 . 60 ALA N N 118.9 0.1 1 109 . 61 VAL H H 8.35 0.01 1 110 . 61 VAL N N 119.8 0.1 1 111 . 62 ASN H H 10.37 0.01 1 112 . 62 ASN N N 129.2 0.1 1 113 . 63 GLY H H 9.04 0.01 1 114 . 63 GLY N N 103.2 0.1 1 115 . 64 VAL H H 8.01 0.01 1 116 . 64 VAL N N 123.9 0.1 1 117 . 65 SER H H 8.67 0.01 1 118 . 65 SER N N 121.4 0.1 1 119 . 66 LEU H H 8.13 0.01 1 120 . 66 LEU N N 125.1 0.1 1 121 . 67 GLU H H 8.21 0.01 1 122 . 67 GLU N N 122.9 0.1 1 123 . 68 GLY H H 9.13 0.01 1 124 . 68 GLY N N 116.1 0.1 1 125 . 69 ALA H H 7.92 0.01 1 126 . 69 ALA N N 122.6 0.1 1 127 . 70 THR H H 8.32 0.01 1 128 . 70 THR N N 112.6 0.1 1 129 . 71 HIS H H 9.17 0.01 1 130 . 71 HIS N N 121.7 0.1 1 131 . 72 LYS H H 8.73 0.01 1 132 . 72 LYS N N 115.8 0.1 1 133 . 73 GLN H H 7.57 0.01 1 134 . 73 GLN N N 117.3 0.1 1 135 . 74 ALA H H 8.50 0.01 1 136 . 74 ALA N N 123.2 0.1 1 137 . 75 VAL H H 8.28 0.01 1 138 . 75 VAL N N 118.2 0.1 1 139 . 76 GLU H H 8.22 0.01 1 140 . 76 GLU N N 119.8 0.1 1 141 . 77 THR H H 7.99 0.01 1 142 . 77 THR N N 116.4 0.1 1 143 . 78 LEU H H 8.03 0.01 1 144 . 78 LEU N N 120.3 0.1 1 145 . 80 ASN H H 8.00 0.01 1 146 . 80 ASN N N 120.7 0.1 1 147 . 81 THR H H 7.56 0.01 1 148 . 81 THR N N 110.1 0.1 1 149 . 82 GLY H H 8.37 0.01 1 150 . 82 GLY N N 109.2 0.1 1 151 . 83 GLN H H 8.16 0.01 1 152 . 83 GLN N N 116.7 0.1 1 153 . 84 VAL H H 7.71 0.01 1 154 . 84 VAL N N 116.4 0.1 1 155 . 85 VAL H H 9.01 0.01 1 156 . 85 VAL N N 128.6 0.1 1 157 . 86 HIS H H 8.71 0.01 1 158 . 86 HIS N N 126.1 0.1 1 159 . 87 LEU H H 8.99 0.01 1 160 . 87 LEU N N 126.7 0.1 1 161 . 88 LEU H H 7.94 0.01 1 162 . 88 LEU N N 124.6 0.1 1 163 . 89 LEU H H 8.93 0.01 1 164 . 89 LEU N N 127.6 0.1 1 165 . 90 GLU H H 8.84 0.01 1 166 . 90 GLU N N 119.2 0.1 1 167 . 91 LYS H H 9.35 0.01 1 168 . 91 LYS N N 129.5 0.1 1 169 . 92 GLY H H 9.63 0.01 1 170 . 92 GLY N N 117.6 0.1 1 171 . 93 GLN H H 8.27 0.01 1 172 . 93 GLN N N 117.0 0.1 1 173 . 94 SER H H 8.41 0.01 1 174 . 94 SER N N 118.6 0.1 1 175 . 96 THR H H 7.74 0.01 1 176 . 96 THR N N 119.5 0.1 1 stop_ save_