data_17925 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; SEVI with Zn ; _BMRB_accession_number 17925 _BMRB_flat_file_name bmr17925.str _Entry_type original _Submission_date 2011-09-07 _Accession_date 2011-09-07 _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 Snell Jessica M. . 2 Sheftic Sarah R. . 3 Alexandrescu Andrei T. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 125 "13C chemical shifts" 39 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-01-17 update BMRB 'update entry citation' 2012-08-23 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 17924 'SEVI without Zn' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Inhibition of semen-derived enhancer of virus infection (SEVI) fibrillogenesis by zinc and copper.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 22907203 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Sheftic Sarah R. . 2 Snell Jessica M. . 3 Jha Suman . . 4 Alexandrescu Andrei T. . stop_ _Journal_abbreviation 'Eur. Biophys. J.' _Journal_name_full 'European biophysics journal : EBJ' _Journal_volume 41 _Journal_issue 9 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 695 _Page_last 704 _Year 2012 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name SEVI _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label SEVI $SEVI Zn $ZN stop_ _System_molecular_weight . _System_physical_state 'intrinsically disordered' _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_SEVI _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common SEVI _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 39 _Mol_residue_sequence ; GIHKQKEKSRLQGGVLVNEI LNHMKRATQIPSYKKLIMY ; loop_ _Residue_seq_code _Residue_label 1 GLY 2 ILE 3 HIS 4 LYS 5 GLN 6 LYS 7 GLU 8 LYS 9 SER 10 ARG 11 LEU 12 GLN 13 GLY 14 GLY 15 VAL 16 LEU 17 VAL 18 ASN 19 GLU 20 ILE 21 LEU 22 ASN 23 HIS 24 MET 25 LYS 26 ARG 27 ALA 28 THR 29 GLN 30 ILE 31 PRO 32 SER 33 TYR 34 LYS 35 LYS 36 LEU 37 ILE 38 MET 39 TYR stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-01-30 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 17193 PAP248-286 100.00 39 100.00 100.00 2.43e-18 BMRB 17346 entity 100.00 39 100.00 100.00 2.43e-18 BMRB 17347 entity 100.00 39 100.00 100.00 2.43e-18 BMRB 17924 SEVI 100.00 39 100.00 100.00 2.43e-18 BMRB 18287 PAP248-286 100.00 39 100.00 100.00 2.43e-18 PDB 1CVI "Crystal Structure Of Human Prostatic Acid Phosphatase" 100.00 342 100.00 100.00 2.03e-17 PDB 1ND5 "Crystal Structures Of Human Prostatic Acid Phosphatase In Complex With A Phosphate Ion And Alpha-Benzylaminobenzylphosphonic Ac" 100.00 354 100.00 100.00 1.95e-17 PDB 1ND6 "Crystal Structures Of Human Prostatic Acid Phosphatase In Complex With A Phosphate Ion And Alpha-Benzylaminobenzylphosphonic Ac" 100.00 354 100.00 100.00 1.95e-17 PDB 2HPA "Structural Origins Of L(+)-Tartrate Inhibition Of Human Prostatic Acid Phosphatase" 100.00 342 100.00 100.00 2.03e-17 PDB 2L3H "Nmr Structure In A Membrane Environment Reveals Putative Amyloidogenic Regions Of The Sevi Precursor Peptide Pap248-286" 97.44 39 100.00 100.00 2.42e-17 PDB 2L77 "Solution Nmr Structure Of Pap248-286 In 50% Tfe" 97.44 39 100.00 100.00 2.42e-17 PDB 2L79 "Solution Nmr Structure Of Pap248-286 In 30% Tfe" 97.44 39 100.00 100.00 2.42e-17 DBJ BAD89417 "Acid phosphatase prostate nirs variant 1 [Homo sapiens]" 100.00 353 100.00 100.00 3.85e-18 DBJ BAG62248 "unnamed protein product [Homo sapiens]" 100.00 353 100.00 100.00 3.85e-18 EMBL CAA36422 "unnamed protein product [Homo sapiens]" 100.00 386 100.00 100.00 3.05e-18 EMBL CAA37673 "unnamed protein product [Homo sapiens]" 100.00 386 100.00 100.00 5.55e-18 GB AAA60021 "prostatic acid phosphatase [Homo sapiens]" 100.00 386 100.00 100.00 1.02e-17 GB AAA60022 "acid phosphatase [Homo sapiens]" 100.00 386 100.00 100.00 6.90e-18 GB AAA69694 "acid phosphatase [Homo sapiens]" 100.00 386 100.00 100.00 1.02e-17 GB AAB60640 "prostatic acid phosphatase [Homo sapiens]" 100.00 386 100.00 100.00 1.02e-17 GB AAH07460 "ACPP protein [Homo sapiens]" 100.00 418 100.00 100.00 1.43e-17 REF NP_001090 "prostatic acid phosphatase isoform PAP precursor [Homo sapiens]" 100.00 386 100.00 100.00 1.02e-17 REF NP_001127666 "prostatic acid phosphatase isoform TM-PAP precursor [Homo sapiens]" 100.00 418 100.00 100.00 1.48e-17 REF NP_001278966 "prostatic acid phosphatase isoform 3 [Homo sapiens]" 100.00 353 100.00 100.00 3.85e-18 REF XP_001115549 "PREDICTED: prostatic acid phosphatase [Macaca mulatta]" 100.00 418 97.44 100.00 1.49e-17 REF XP_001148736 "PREDICTED: prostatic acid phosphatase [Pan troglodytes]" 100.00 418 97.44 97.44 6.83e-17 SP P15309 "RecName: Full=Prostatic acid phosphatase; Short=PAP; AltName: Full=5'-nucleotidase; Short=5'-NT; AltName: Full=Ecto-5'-nucleoti" 100.00 386 100.00 100.00 1.02e-17 stop_ save_ ############# # Ligands # ############# save_ZN _Saveframe_category ligand _Mol_type non-polymer _Name_common "ZN (ZINC ION)" _BMRB_code . _PDB_code ZN _Molecular_mass 65.409 _Mol_charge 2 _Mol_paramagnetic . _Mol_aromatic no _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Tue Jun 9 16:52:42 2009 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons ZN ZN ZN . 2 . ? 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 $SEVI 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 $SEVI 'chemical synthesis' . . . . . 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 $SEVI 3.0 mM 'natural abundance' $ZN 4.0 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_VNMRJ _Saveframe_category software _Name VNMRJ _Version . loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_Felix _Saveframe_category software _Name Felix _Version . loop_ _Vendor _Address _Electronic_address 'Accelrys Software Inc.' . . stop_ loop_ _Task 'data analysis' 'peak picking' 'chemical shift assignment' 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 $sample_1 save_ save_2D_1H-13C_HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_NMR_spectrometer_expt _Saveframe_category NMR_applied_experiment _Experiment_name . _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 273 . K pH 5.6 . pH pressure 1 . atm 'ionic strength' 0 . M 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 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_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-15N HSQC' '2D 1H-13C HSQC' '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 SEVI _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 CA C 43.06 0.10 1 2 2 2 ILE CA C 61.31 0.10 1 3 3 3 HIS CA C 55.33 0.10 1 4 4 4 LYS H H 8.59 0.05 1 5 4 4 LYS HA H 4.25 0.05 1 6 4 4 LYS HB2 H 1.76 0.05 2 7 4 4 LYS CA C 56.48 0.10 1 8 5 5 GLN H H 8.29 0.05 1 9 5 5 GLN HA H 4.21 0.05 1 10 5 5 GLN HB2 H 2.03 0.05 2 11 5 5 GLN CA C 56.38 0.10 1 12 6 6 LYS H H 8.23 0.05 1 13 6 6 LYS HA H 4.25 0.05 1 14 6 6 LYS HB2 H 1.73 0.05 2 15 6 6 LYS CA C 56.48 0.10 1 16 7 7 GLU H H 8.59 0.05 1 17 7 7 GLU HA H 4.26 0.05 1 18 7 7 GLU HB2 H 2.08 0.05 2 19 7 7 GLU HB3 H 1.97 0.05 2 20 7 7 GLU HG2 H 2.35 0.05 2 21 7 7 GLU CA C 56.48 0.10 1 22 8 8 LYS H H 8.48 0.05 1 23 8 8 LYS HA H 4.36 0.05 1 24 8 8 LYS HB2 H 1.60 0.05 2 25 8 8 LYS CA C 56.17 0.10 1 26 9 9 SER H H 8.44 0.05 1 27 9 9 SER HA H 4.42 0.05 1 28 9 9 SER HB2 H 3.84 0.05 2 29 9 9 SER CA C 58.37 0.10 1 30 10 10 ARG H H 8.55 0.05 1 31 10 10 ARG HA H 4.36 0.05 1 32 10 10 ARG HB2 H 1.62 0.05 2 33 10 10 ARG HB3 H 1.75 0.05 2 34 10 10 ARG HG2 H 1.77 0.05 2 35 10 10 ARG CA C 56.17 0.10 1 36 11 11 LEU H H 8.36 0.05 1 37 11 11 LEU HA H 4.39 0.05 1 38 11 11 LEU HB2 H 1.62 0.05 2 39 11 11 LEU HB3 H 1.53 0.05 2 40 11 11 LEU HG H 1.86 0.05 1 41 11 11 LEU HD1 H 0.89 0.05 2 42 11 11 LEU CA C 55.02 0.10 1 43 12 12 GLN H H 8.55 0.05 1 44 12 12 GLN HA H 4.36 0.05 1 45 12 12 GLN HB2 H 1.99 0.05 2 46 12 12 GLN HB3 H 2.09 0.05 2 47 12 12 GLN HG2 H 2.35 0.05 2 48 12 12 GLN CA C 56.38 0.10 1 49 13 13 GLY H H 8.67 0.05 1 50 13 13 GLY HA2 H 3.96 0.05 2 51 13 13 GLY CA C 45.36 0.10 1 52 14 14 GLY H H 8.16 0.05 1 53 14 14 GLY HA2 H 3.95 0.05 2 54 14 14 GLY CA C 45.05 0.10 1 55 15 15 VAL H H 8.02 0.05 1 56 15 15 VAL HA H 4.10 0.05 1 57 15 15 VAL HB H 2.06 0.05 1 58 15 15 VAL HG1 H 0.92 0.05 2 59 15 15 VAL CA C 62.15 0.10 1 60 16 16 LEU H H 8.45 0.05 1 61 16 16 LEU HA H 4.26 0.05 1 62 16 16 LEU CA C 54.91 0.10 1 63 17 17 VAL H H 8.29 0.05 1 64 17 17 VAL HA H 4.03 0.05 1 65 17 17 VAL HG1 H 0.91 0.05 2 66 17 17 VAL CA C 62.57 0.10 1 67 18 18 ASN H H 8.54 0.05 1 68 18 18 ASN HA H 4.65 0.05 1 69 18 18 ASN HB2 H 2.81 0.05 2 70 18 18 ASN HB3 H 2.72 0.05 2 71 18 18 ASN CA C 53.44 0.10 1 72 19 19 GLU H H 8.48 0.05 1 73 19 19 GLU HB2 H 2.04 0.05 2 74 19 19 GLU HB3 H 1.96 0.05 2 75 19 19 GLU HG2 H 2.33 0.05 2 76 19 19 GLU CA C 57.22 0.10 1 77 20 20 ILE H H 8.17 0.05 1 78 20 20 ILE HA H 4.04 0.05 1 79 20 20 ILE HB H 1.85 0.05 1 80 20 20 ILE CA C 62.15 0.10 1 81 21 21 LEU H H 8.36 0.05 1 82 21 21 LEU HA H 4.39 0.05 1 83 21 21 LEU HB2 H 1.62 0.05 2 84 21 21 LEU HB3 H 1.53 0.05 2 85 21 21 LEU CA C 55.02 0.10 1 86 22 22 ASN CA C 53.65 0.10 1 87 23 23 HIS CA C 56.17 0.10 1 88 24 24 MET H H 8.08 0.05 1 89 24 24 MET HA H 4.39 0.05 1 90 24 24 MET HB2 H 2.06 0.05 2 91 24 24 MET CA C 55.85 0.10 1 92 25 25 LYS H H 8.30 0.05 1 93 25 25 LYS HA H 4.20 0.05 1 94 25 25 LYS HB2 H 1.78 0.05 2 95 25 25 LYS CA C 56.48 0.10 1 96 26 26 ARG H H 8.40 0.05 1 97 26 26 ARG HA H 4.30 0.05 1 98 26 26 ARG HB2 H 1.90 0.05 2 99 26 26 ARG HG2 H 1.75 0.05 2 100 26 26 ARG HD2 H 3.91 0.05 2 101 26 26 ARG CA C 56.17 0.10 1 102 27 27 ALA H H 8.50 0.05 1 103 27 27 ALA HB H 1.40 0.05 1 104 27 27 ALA CA C 52.50 0.10 1 105 28 28 THR H H 8.23 . 1 106 28 28 THR HA H 4.25 . 1 107 28 28 THR HB H 4.18 . 1 108 28 28 THR HG2 H 1.23 0.05 1 109 28 28 THR CA C 61.94 0.10 1 110 29 29 GLN H H 8.63 0.05 1 111 29 29 GLN HA H 4.26 0.05 1 112 29 29 GLN HB2 H 1.98 0.05 2 113 29 29 GLN HB3 H 2.08 0.05 2 114 29 29 GLN CA C 55.75 0.10 1 115 30 30 ILE H H 8.43 0.05 1 116 30 30 ILE HA H 4.40 0.05 1 117 30 30 ILE HB H 1.87 0.05 1 118 30 30 ILE HG12 H 1.18 0.05 2 119 30 30 ILE HG2 H 0.96 0.05 4 120 30 30 ILE HD1 H 0.87 0.05 4 121 30 30 ILE CA C 61.21 0.10 1 122 31 31 PRO CA C 63.20 0.10 1 123 32 32 SER H H 8.41 0.05 1 124 32 32 SER HB2 H 3.96 0.05 2 125 32 32 SER CA C 58.16 0.10 1 126 33 33 TYR H H 8.23 0.05 1 127 33 33 TYR HA H 4.55 0.05 1 128 33 33 TYR HB2 H 3.01 0.05 2 129 33 33 TYR CA C 57.95 0.10 1 130 34 34 LYS H H 8.10 0.05 1 131 34 34 LYS HA H 4.19 0.05 1 132 34 34 LYS HB2 H 1.63 0.05 2 133 34 34 LYS HB3 H 1.73 0.05 2 134 34 34 LYS HG2 H 1.30 0.05 2 135 34 34 LYS HE2 H 2.95 0.05 2 136 34 34 LYS CA C 56.38 0.10 1 137 35 35 LYS H H 8.14 0.05 1 138 35 35 LYS HA H 4.19 0.05 1 139 35 35 LYS HB2 H 1.63 0.05 2 140 35 35 LYS HB3 H 1.73 0.05 2 141 35 35 LYS CA C 56.38 0.10 1 142 36 36 LEU H H 8.32 0.05 1 143 36 36 LEU HA H 4.32 0.05 1 144 36 36 LEU HB2 H 1.60 0.05 2 145 36 36 LEU HD1 H 0.91 0.05 2 146 36 36 LEU CA C 55.12 0.10 1 147 37 37 ILE H H 8.20 . 1 148 37 37 ILE HA H 4.05 . 1 149 37 37 ILE HB H 1.75 . 1 150 37 37 ILE HG12 H 1.43 . . 151 37 37 ILE HG13 H 1.13 . . 152 37 37 ILE HD1 H 0.71 0.05 4 153 37 37 ILE CA C 60.89 0.10 1 154 38 38 MET H H 8.40 . 1 155 38 38 MET HA H 4.43 . 1 156 38 38 MET HB2 H 1.91 . . 157 38 38 MET HG2 H 2.47 . . 158 38 38 MET HG3 H 2.38 . . 159 38 38 MET CA C 54.91 0.10 1 160 39 39 TYR H H 8.28 . 1 161 39 39 TYR HA H 4.53 . 1 162 39 39 TYR HB2 H 3.09 . . 163 39 39 TYR HB3 H 2.91 . . 164 39 39 TYR CA C 57.64 0.10 1 stop_ loop_ _Atom_shift_assign_ID_ambiguity 119 '119,119,120,120,120' '152,152,152' stop_ save_