data_20044 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR structure of the Interleukin-8 C-terminal domain in solution with SDS micelles ; _BMRB_accession_number 20044 _BMRB_flat_file_name bmr20044.str _Entry_type new _Submission_date 2008-08-26 _Accession_date 2008-08-26 _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 Bourbigot Sarah . . 2 Booth Valerie . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 134 "15N chemical shifts" 4 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-01-25 update author 'complete entry citation' 2009-10-14 update author 'update entry citation' 2009-10-12 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structure of chemokine-derived antimicrobial Peptide interleukin-8alpha and interaction with detergent micelles and oriented lipid bilayers.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 19813761 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Bourbigot Sarah . . 2 Fardy Liam . . 3 Waring Alan J. . 4 Yeaman Michael R. . 5 Booth Valerie . . stop_ _Journal_abbreviation Biochemistry _Journal_name_full Biochemistry _Journal_volume 48 _Journal_issue 44 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 10509 _Page_last 10521 _Year 2009 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Interleukin-8 C-terminal domain' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'subunit 1' $interleukin-8_C-terminal_domain 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_interleukin-8_C-terminal_domain _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common interleukin-8_C-terminal_domain _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 19 _Mol_residue_sequence KENWVQRVVEKFLKRAENS loop_ _Residue_seq_code _Residue_label 1 LYS 2 GLU 3 ASN 4 TRP 5 VAL 6 GLN 7 ARG 8 VAL 9 VAL 10 GLU 11 LYS 12 PHE 13 LEU 14 LYS 15 ARG 16 ALA 17 GLU 18 ASN 19 SER stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-01-29 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 280 "interleukin 8" 100.00 72 100.00 100.00 2.41e-03 PDB 1ICW "Interleukin-8, Mutant With Glu 38 Replaced By Cys And Cys 50 Replaced By Ala" 100.00 72 100.00 100.00 2.22e-03 PDB 1IKL "Nmr Study Of Monomeric Human Interleukin-8 (Minimized Average Structure)" 100.00 72 100.00 100.00 2.43e-03 PDB 1IKM "Nmr Study Of Monomeric Human Interleukin-8 (30 Structures)" 100.00 72 100.00 100.00 2.43e-03 PDB 1IL8 "Three-Dimensional Structure Of Interleukin 8 In Solution" 100.00 72 100.00 100.00 2.41e-03 PDB 1ILP "Cxcr-1 N-Terminal Peptide Bound To Interleukin-8" 100.00 72 100.00 100.00 2.41e-03 PDB 1ILQ "Cxcr-1 N-Terminal Peptide Bound To Interleukin-8 (Minimized Mean)" 100.00 72 100.00 100.00 2.41e-03 PDB 1QE6 "Interleukin-8 With An Added Disulfide Between Residues 5 And 33 (l5c/h33c)" 100.00 72 100.00 100.00 2.07e-03 PDB 2IL8 "Three-Dimensional Structure Of Interleukin 8 In Solution" 100.00 72 100.00 100.00 2.41e-03 PDB 3IL8 "Crystal Structure Of Interleukin 8: Symbiosis Of Nmr And Crystallography" 100.00 72 100.00 100.00 2.41e-03 DBJ BAA03245 "LUCT/interleukin-8 [Homo sapiens]" 100.00 99 100.00 100.00 1.53e-03 DBJ BAG34815 "unnamed protein product [Homo sapiens]" 100.00 99 100.00 100.00 1.53e-03 DBJ BAJ20387 "interleukin 8 [synthetic construct]" 100.00 99 100.00 100.00 1.53e-03 EMBL CAA68742 "MDNCF precursor (AA -27 to 72) [Homo sapiens]" 100.00 99 100.00 100.00 1.53e-03 EMBL CAA77745 "interleukin 8 [Homo sapiens]" 89.47 97 100.00 100.00 4.32e-02 EMBL CAG46948 "IL8 [Homo sapiens]" 100.00 99 100.00 100.00 1.53e-03 GB AAA35611 "beta-thromboglobulin-like protein precursor [Homo sapiens]" 100.00 99 100.00 100.00 1.53e-03 GB AAA36323 "monocyte-derived neutrophil-activating protein precursor [Homo sapiens]" 100.00 99 100.00 100.00 1.53e-03 GB AAA59158 "interleukin 8 [Homo sapiens]" 100.00 99 100.00 100.00 1.53e-03 GB AAA74722 "neutrophil-activating factor [synthetic construct]" 100.00 73 100.00 100.00 2.35e-03 GB AAB01177 "interleukin-8 [synthetic construct]" 100.00 73 100.00 100.00 2.35e-03 REF NP_000575 "interleukin-8 precursor [Homo sapiens]" 100.00 99 100.00 100.00 1.53e-03 REF XP_001156432 "PREDICTED: interleukin-8 [Pan troglodytes]" 100.00 99 100.00 100.00 1.53e-03 REF XP_002814902 "PREDICTED: interleukin-8 isoform X1 [Pongo abelii]" 94.74 101 100.00 100.00 6.16e-03 REF XP_002814903 "PREDICTED: interleukin-8 [Pongo abelii]" 94.74 101 100.00 100.00 6.16e-03 REF XP_003832383 "PREDICTED: interleukin-8 [Pan paniscus]" 100.00 99 100.00 100.00 1.53e-03 SP P10145 "RecName: Full=Interleukin-8; Short=IL-8; AltName: Full=C-X-C motif chemokine 8; AltName: Full=Chemokine (C-X-C motif) ligand 8;" 100.00 99 100.00 100.00 1.53e-03 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $interleukin-8_C-terminal_domain . . . . . . 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 _Details $interleukin-8_C-terminal_domain 'chemical synthesis' . . . . . 'solid phase synthesis employing Fmoc (O-fluorenylmethyl-oxycarbonyl) chemistry' 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 $interleukin-8_C-terminal_domain 1.5 mM [U-15N]-Leu;[U-15N]-Ala;[U-15N]-Val H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' DSS 0.4 mM 'natural abundance' 'sodium azide' 0.4 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CNS _Saveframe_category software _Name CNS _Version 1.1 loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task 'structure calculation' refinement stop_ _Details . save_ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version 3.110 loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'data analysis' 'peak picking' stop_ _Details . save_ save_ProcheckNMR _Saveframe_category software _Name ProcheckNMR _Version . loop_ _Vendor _Address _Electronic_address 'Laskowski and MacArthur' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 500 _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-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-15N_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _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_ save_2D_1H-1H_NOESY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_7 _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 temperature 298.15 . K pH 5 . pH pressure 1 . atm stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 303.15 . K pH 5 . pH pressure 1 . atm stop_ save_ save_sample_conditions_3 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 308.15 . K pH 5 . pH pressure 1 . atm 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 N 15 'methyl protons' ppm 0.00 n/a 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-1H TOCSY' '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_3 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'subunit 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 1 1 LYS HA H 4.112 0.020 1 2 1 1 LYS HB2 H 1.911 0.020 2 3 1 1 LYS HB3 H 1.911 0.020 2 4 1 1 LYS HG2 H 1.472 0.020 2 5 1 1 LYS HG3 H 1.472 0.020 2 6 2 2 GLU H H 8.478 0.020 1 7 2 2 GLU HA H 4.321 0.020 1 8 2 2 GLU HB2 H 1.604 0.020 2 9 2 2 GLU HB3 H 1.714 0.020 2 10 2 2 GLU HG2 H 2.238 0.020 2 11 2 2 GLU HG3 H 2.238 0.020 2 12 3 3 ASN H H 8.378 0.020 1 13 3 3 ASN HA H 4.765 0.020 1 14 3 3 ASN HB2 H 2.921 0.020 2 15 3 3 ASN HB3 H 2.921 0.020 2 16 3 3 ASN HD21 H 6.725 0.020 2 17 3 3 ASN HD22 H 7.463 0.020 2 18 4 4 TRP H H 8.006 0.020 1 19 4 4 TRP HA H 4.264 0.020 1 20 4 4 TRP HB2 H 3.301 0.020 2 21 4 4 TRP HB3 H 3.301 0.020 2 22 4 4 TRP HD1 H 7.436 0.020 1 23 4 4 TRP HE1 H 9.897 0.020 1 24 4 4 TRP HE3 H 7.396 0.020 1 25 4 4 TRP HH2 H 7.100 0.020 1 26 4 4 TRP HZ2 H 7.418 0.020 1 27 4 4 TRP HZ3 H 6.942 0.020 1 28 5 5 VAL H H 7.556 0.020 1 29 5 5 VAL HA H 3.391 0.020 1 30 5 5 VAL HB H 2.016 0.020 1 31 5 5 VAL HG1 H 0.833 0.020 2 32 5 5 VAL HG2 H 0.656 0.020 2 33 5 5 VAL N N 118.484 0.050 1 34 6 6 GLN H H 7.724 0.020 1 35 6 6 GLN HA H 3.864 0.020 1 36 6 6 GLN HB2 H 2.101 0.020 2 37 6 6 GLN HB3 H 2.101 0.020 2 38 6 6 GLN HE21 H 6.673 0.020 2 39 6 6 GLN HE22 H 7.330 0.020 2 40 6 6 GLN HG2 H 2.356 0.020 2 41 6 6 GLN HG3 H 2.444 0.020 2 42 7 7 ARG H H 7.795 0.020 1 43 7 7 ARG HA H 4.044 0.020 1 44 7 7 ARG HB2 H 1.918 0.020 2 45 7 7 ARG HB3 H 1.918 0.020 2 46 7 7 ARG HD2 H 3.087 0.020 2 47 7 7 ARG HD3 H 3.087 0.020 2 48 7 7 ARG HE H 6.987 0.020 1 49 7 7 ARG HG2 H 1.649 0.020 2 50 7 7 ARG HG3 H 1.649 0.020 2 51 7 7 ARG HH11 H 6.506 0.020 2 52 7 7 ARG HH12 H 6.506 0.020 2 53 7 7 ARG HH21 H 6.506 0.020 2 54 7 7 ARG HH22 H 6.506 0.020 2 55 8 8 VAL H H 8.081 0.020 1 56 8 8 VAL HA H 3.745 0.020 1 57 8 8 VAL HB H 2.345 0.020 1 58 8 8 VAL HG1 H 1.119 0.020 2 59 8 8 VAL HG2 H 1.119 0.020 2 60 8 8 VAL N N 119.159 0.050 1 61 9 9 VAL H H 8.370 0.020 1 62 9 9 VAL HA H 3.612 0.020 1 63 9 9 VAL HB H 2.209 0.020 1 64 9 9 VAL HG1 H 1.044 0.020 2 65 9 9 VAL HG2 H 1.044 0.020 2 66 10 10 GLU H H 8.254 0.020 1 67 10 10 GLU HA H 3.997 0.020 1 68 10 10 GLU HB2 H 2.527 0.020 2 69 10 10 GLU HB3 H 2.527 0.020 2 70 10 10 GLU HG2 H 2.155 0.020 2 71 10 10 GLU HG3 H 2.155 0.020 2 72 11 11 LYS H H 7.679 0.020 1 73 11 11 LYS HA H 4.040 0.020 1 74 11 11 LYS HB2 H 1.915 0.020 2 75 11 11 LYS HB3 H 1.915 0.020 2 76 11 11 LYS HD2 H 1.409 0.020 2 77 11 11 LYS HD3 H 1.409 0.020 2 78 11 11 LYS HG2 H 1.296 0.020 2 79 11 11 LYS HG3 H 1.296 0.020 2 80 12 12 PHE H H 8.119 0.020 1 81 12 12 PHE HA H 4.347 0.020 1 82 12 12 PHE HB2 H 3.164 0.020 2 83 12 12 PHE HB3 H 3.164 0.020 2 84 12 12 PHE HD1 H 7.250 0.020 3 85 12 12 PHE HD2 H 7.250 0.020 3 86 12 12 PHE HE1 H 7.210 0.020 3 87 12 12 PHE HE2 H 7.210 0.020 3 88 13 13 LEU H H 8.495 0.020 1 89 13 13 LEU HA H 4.149 0.020 1 90 13 13 LEU HB2 H 1.890 0.020 2 91 13 13 LEU HB3 H 1.890 0.020 2 92 13 13 LEU HD1 H 0.950 0.020 2 93 13 13 LEU HD2 H 0.950 0.020 2 94 13 13 LEU HG H 1.936 0.020 1 95 13 13 LEU N N 118.960 0.050 1 96 14 14 LYS H H 7.858 0.020 1 97 14 14 LYS HA H 4.177 0.020 1 98 14 14 LYS HB2 H 1.764 0.020 2 99 14 14 LYS HB3 H 1.764 0.020 2 100 14 14 LYS HD2 H 1.547 0.020 2 101 14 14 LYS HD3 H 1.547 0.020 2 102 14 14 LYS HE2 H 3.049 0.020 2 103 14 14 LYS HE3 H 3.049 0.020 2 104 14 14 LYS HG2 H 1.469 0.020 2 105 14 14 LYS HG3 H 1.469 0.020 2 106 15 15 ARG H H 7.601 0.020 1 107 15 15 ARG HA H 4.176 0.020 1 108 15 15 ARG HB2 H 1.886 0.020 2 109 15 15 ARG HB3 H 1.886 0.020 2 110 15 15 ARG HD2 H 3.175 0.020 2 111 15 15 ARG HD3 H 3.175 0.020 2 112 15 15 ARG HE H 7.156 0.020 1 113 15 15 ARG HG2 H 1.644 0.020 2 114 15 15 ARG HG3 H 1.644 0.020 2 115 15 15 ARG HH11 H 6.603 0.020 2 116 15 15 ARG HH12 H 6.603 0.020 2 117 15 15 ARG HH21 H 6.603 0.020 2 118 15 15 ARG HH22 H 6.603 0.020 2 119 16 16 ALA H H 8.037 0.020 1 120 16 16 ALA HA H 4.231 0.020 1 121 16 16 ALA HB H 1.353 0.020 1 122 16 16 ALA N N 121.919 0.050 1 123 17 17 GLU H H 7.914 0.020 1 124 17 17 GLU HA H 4.283 0.020 1 125 17 17 GLU HB2 H 2.074 0.020 2 126 17 17 GLU HB3 H 2.074 0.020 2 127 17 17 GLU HG2 H 2.448 0.020 2 128 17 17 GLU HG3 H 2.448 0.020 2 129 18 18 ASN H H 8.071 0.020 1 130 18 18 ASN HA H 4.779 0.020 1 131 18 18 ASN HB2 H 2.894 0.020 2 132 18 18 ASN HB3 H 2.753 0.020 2 133 18 18 ASN HD21 H 6.832 0.020 2 134 18 18 ASN HD22 H 7.525 0.020 2 135 19 19 SER H H 7.788 0.020 1 136 19 19 SER HA H 4.285 0.020 1 137 19 19 SER HB2 H 3.867 0.020 2 138 19 19 SER HB3 H 3.867 0.020 2 stop_ save_