data_5877 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solid State NMR Structure of the Major Coat Protein in Bacteriophage Pf1 ; _BMRB_accession_number 5877 _BMRB_flat_file_name bmr5877.str _Entry_type original _Submission_date 2003-07-21 _Accession_date 2003-07-22 _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 Thiriot D. S. . 2 Opella S. J. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 coupling_constants 1 stop_ loop_ _Data_type _Data_type_count "15N chemical shifts" 43 "coupling constants" 43 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2007-02-22 update BMRB 'add relationship loop' 2004-10-25 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 15138 '13C and 15N resonance assignments' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structure of the coat protein in Pf1 bacteriophage determined by solid-state NMR spectroscopy. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 15288792 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Thiriot D. S. . 2 Nevzorov A. A. . 3 Zagyanskiy L. . . 4 Wu C. H. . 5 Opella S. J. . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_volume 341 _Journal_issue 3 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 869 _Page_last 879 _Year 2004 _Details . loop_ _Keyword 'Virus/Viral protein' stop_ save_ ################################## # Molecular system description # ################################## save_system_Pf3_major_coat_protein _Saveframe_category molecular_system _Mol_system_name 'Bacteriophage Pf1 major coat protein' _Abbreviation_common 'Pf3 major coat protein' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'Pf1 major coat protein' $Pf1_coat_protein stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_Pf1_coat_protein _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'Pf1 phage major coat protein' _Abbreviation_common 'Pf1 coat protein' _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 46 _Mol_residue_sequence ; GVIDTSAVESAITDGQGDMK AIGGYIVGALVILAVAGLIY SMLRKA ; loop_ _Residue_seq_code _Residue_label 1 GLY 2 VAL 3 ILE 4 ASP 5 THR 6 SER 7 ALA 8 VAL 9 GLU 10 SER 11 ALA 12 ILE 13 THR 14 ASP 15 GLY 16 GLN 17 GLY 18 ASP 19 MET 20 LYS 21 ALA 22 ILE 23 GLY 24 GLY 25 TYR 26 ILE 27 VAL 28 GLY 29 ALA 30 LEU 31 VAL 32 ILE 33 LEU 34 ALA 35 VAL 36 ALA 37 GLY 38 LEU 39 ILE 40 TYR 41 SER 42 MET 43 LEU 44 ARG 45 LYS 46 ALA stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-01-28 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 15138 Pf1_phage_coat_protein 100.00 46 100.00 100.00 1.03e-20 PDB 1IFM "Two Forms Of Pf1 Inovirus: X-Ray Diffraction Studies On A Structural Phase Transition And A Calculated Libration Normal Mode Of" 100.00 46 100.00 100.00 1.03e-20 PDB 1IFN "Two Forms Of Pf1 Inovirus: X-Ray Diffraction Studies On A Structural Phase Transition And A Calculated Libration Normal Mode Of" 100.00 46 100.00 100.00 1.03e-20 PDB 1PFI "Pf1 Virus Structure: Helical Coat Protein And Dna With Paraxial Phosphates" 100.00 46 100.00 100.00 1.03e-20 PDB 1PJF "Solid State Nmr Structure Of The Pf1 Major Coat Protein In Magnetically Aligned Bacteriophage" 100.00 46 100.00 100.00 1.03e-20 PDB 1QL1 "Inovirus (Filamentous Bacteriophage) Strain Pf1 Major Coat Protein Assembly" 100.00 46 100.00 100.00 1.03e-20 PDB 1QL2 "Inovirus (Filamentous Bacteriophage) Strain Pf1 Major Coat Protein Assembly" 100.00 46 100.00 100.00 1.03e-20 PDB 1ZN5 "Solid State Nmr Structure Of The Low-Temperature Form Of The Pf1 Major Coat Protein In Magnetically Aligned Bacteriophage" 100.00 46 100.00 100.00 1.03e-20 PDB 2IFM "Pf1 Filamentous Bacteriophage: Refinement Of A Molecular Model By Simulated Annealing Using 3.3 Angstroms Resolution X-Ray Fibr" 100.00 46 100.00 100.00 1.03e-20 PDB 2IFN "Pf1 Filamentous Bacteriophage: Refinement Of A Molecular Model By Simulated Annealing Using 3.3 Angstroms Resolution X-Ray Fibr" 100.00 46 100.00 100.00 1.03e-20 PDB 2KLV "Membrane-Bound Structure Of The Pf1 Major Coat Protein In Dhpc Micelle" 100.00 46 100.00 100.00 1.03e-20 PDB 2KSJ "Structure And Dynamics Of The Membrane-Bound Form Of Pf1 Coat Protein: Implications For Structural Rearrangement During Virus A" 100.00 46 100.00 100.00 1.03e-20 PDB 2XKM "Consensus Structure Of Pf1 Filamentous Bacteriophage From X- Ray Fibre Diffraction And Solid-State Nmr" 100.00 46 100.00 100.00 1.03e-20 PDB 3IFM "Pf1 Filamentous Bacteriophage: Refinement Of A Molecular Model By Simulated Annealing Using 3.3 Angstroms Resolution X-Ray Fibr" 100.00 46 100.00 100.00 1.03e-20 PDB 4IFM "Pf1 Filamentous Bacteriophage: Refinement Of A Molecular Model By Simulated Annealing Using 3.3 Angstroms Resolution X-Ray Fibr" 100.00 46 100.00 100.00 1.03e-20 EMBL CAA36331 "major coat protein [Pseudomonas phage Pf1]" 100.00 82 100.00 100.00 3.26e-21 EMBL CCQ85809 "hypothetical protein PA18A_2405 [Pseudomonas aeruginosa 18A]" 100.00 82 100.00 100.00 3.26e-21 EMBL CDH73426 "putative secreted protein [Pseudomonas aeruginosa MH38]" 100.00 82 100.00 100.00 3.55e-21 EMBL CDO83853 "coat protein B of bacteriophage Pf1) [Pseudomonas aeruginosa]" 100.00 82 100.00 100.00 3.26e-21 GB AAG04112 "coat protein B of bacteriophage Pf1 [Pseudomonas aeruginosa PAO1]" 100.00 82 100.00 100.00 3.26e-21 GB AAT50608 "PA0723, partial [synthetic construct]" 100.00 83 100.00 100.00 3.88e-21 GB ACS36651 "phage coat protein B [Pseudomonas aeruginosa PAO1]" 100.00 82 100.00 100.00 3.26e-21 GB AGV62109 "capsid protein G8P [Pseudomonas aeruginosa PAO581]" 100.00 82 100.00 100.00 3.26e-21 GB AGV64452 "capsid protein G8P [Pseudomonas aeruginosa c7447m]" 100.00 82 100.00 100.00 3.26e-21 PRF 754922A protein,coat 100.00 46 97.83 100.00 3.02e-20 REF NP_039603 "major coat protein [Pseudomonas phage Pf1]" 100.00 82 100.00 100.00 3.26e-21 REF NP_249414 "coat protein B of bacteriophage Pf1 [Pseudomonas aeruginosa PAO1]" 100.00 82 100.00 100.00 3.26e-21 REF NP_955532 "major coat protein [Pseudomonas phage Pf1]" 100.00 46 100.00 100.00 1.03e-20 REF WP_003125072 "MULTISPECIES: capsid protein [Pseudomonas]" 100.00 82 100.00 100.00 3.26e-21 REF WP_019372527 "hypothetical protein, partial [Pseudomonas aeruginosa]" 50.00 56 100.00 100.00 1.31e-05 SP P03621 "RecName: Full=Capsid protein G8P; AltName: Full=Coat protein B; AltName: Full=Gene 8 protein; Short=G8P; AltName: Full=Major co" 100.00 82 100.00 100.00 3.26e-21 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _ATCC_number $Pf1_coat_protein 'Pseudomonas phage Pf1' 10871 Viruses . Inovirus 'Pseudomonas phage Pf1' 25102-B1 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 $Pf1_coat_protein 'purified from the natural source' . . . . . 'Bacterial Host was Pseudomonas aeruginosa, ATCC# 25102.' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type gel _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Pf1_coat_protein 50 mg/mL [U-15N] 'sodium borate buffer' 5 mM . H2O . M . stop_ save_ ############################ # Computer software used # ############################ save_FELIX _Saveframe_category software _Name FELIX _Version 2000.1 loop_ _Task processing stop_ _Details Accelrys save_ save_XWINNMR_MacNMR_NTNMR _Saveframe_category software _Name 'XWINNMR, MacNMR, NTNMR' _Version . loop_ _Task collection stop_ _Details 'Bruker, Tecmag' save_ save_MATLAB_script _Saveframe_category software _Name 'MATLAB script' _Version 6.5 loop_ _Task 'structure solution' stop_ _Details Nevzorov save_ save_MATLAB_scripts _Saveframe_category software _Name 'MATLAB scripts' _Version 6.5 loop_ _Task refinement stop_ _Details 'Nevzorov, Thiriot' save_ save_SCWRL_modified _Saveframe_category software _Name SCWRL _Version '2.95 - Blue Horizon modified' loop_ _Task refinement stop_ _Details 'Bower, Cohen, Dunbrack, Majumdar, Chukkapalli' save_ save_SCWRL _Saveframe_category software _Name SCWRL _Version 2.95 loop_ _Task refinement stop_ _Details 'Bower, Cohen, Dunbrack' save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AVANCE _Field_strength 750 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Homebuilt _Model Apollo _Field_strength 550 _Details . save_ ############################# # NMR applied experiments # ############################# save_PISEMA_1 _Saveframe_category NMR_applied_experiment _Experiment_name PISEMA _Sample_label . save_ save_Magic_Sammy_2 _Saveframe_category NMR_applied_experiment _Experiment_name 'Magic Sammy' _Sample_label . save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name PISEMA _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name 'Magic Sammy' _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 8 0.2 n/a temperature 303 1 K pressure 1 . atm stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _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 'ammonium sulfate' N 15 'ammonium ion' ppm 26.8 external direct cylindrical external perpendicular 1.0 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_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'Pf1 major coat protein' _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 VAL N N 164.1 0.5 . 2 . 3 ILE N N 91.4 0.5 . 3 . 4 ASP N N 90.3 0.5 . 4 . 5 THR N N 101.5 0.5 . 5 . 6 SER N N 153.6 0.5 . 6 . 7 ALA N N 171 0.5 . 7 . 8 VAL N N 203.1 0.5 . 8 . 9 GLU N N 221.4 0.5 . 9 . 10 SER N N 196.2 0.5 . 10 . 11 ALA N N 162.8 0.5 . 11 . 12 ILE N N 188.3 0.5 . 12 . 13 THR N N 217.8 0.5 . 13 . 14 ASP N N 223.7 0.5 . 14 . 17 GLY N N 204.4 0.5 . 15 . 18 ASP N N 183.2 0.5 . 16 . 19 MET N N 175.5 0.5 . 17 . 20 LYS N N 211.1 0.5 . 18 . 21 ALA N N 210.2 0.5 . 19 . 22 ILE N N 164.3 0.5 . 20 . 23 GLY N N 180.4 0.5 . 21 . 24 GLY N N 213.1 0.5 . 22 . 25 TYR N N 190.9 0.5 . 23 . 26 ILE N N 166.9 0.5 . 24 . 27 VAL N N 191 0.5 . 25 . 28 GLY N N 204.4 0.5 . 26 . 29 ALA N N 181.8 0.5 . 27 . 30 LEU N N 176.9 0.5 . 28 . 31 VAL N N 205.2 0.5 . 29 . 32 ILE N N 219.4 0.5 . 30 . 33 LEU N N 174.3 0.5 . 31 . 34 ALA N N 192.1 0.5 . 32 . 35 VAL N N 215 0.5 . 33 . 36 ALA N N 208.7 0.5 . 34 . 37 GLY N N 158.9 0.5 . 35 . 38 LEU N N 212.6 0.5 . 36 . 39 ILE N N 219.9 0.5 . 37 . 40 TYR N N 188.8 0.5 . 38 . 41 SER N N 182.8 0.5 . 39 . 42 MET N N 221 0.5 . 40 . 43 LEU N N 203.6 0.5 . 41 . 44 ARG N N 143 0.5 . 42 . 45 LYS N N 142.6 0.5 . 43 . 46 ALA N N 201.1 0.5 . stop_ save_ ######################## # Coupling constants # ######################## save_coupling_constants_1 _Saveframe_category coupling_constants _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Spectrometer_frequency_1H 750 _Mol_system_component_name 'Pf1 major coat protein' _Text_data_format . _Text_data . loop_ _Coupling_constant_ID _Coupling_constant_code _Atom_one_residue_seq_code _Atom_one_residue_label _Atom_one_name _Atom_two_residue_seq_code _Atom_two_residue_label _Atom_two_name _Coupling_constant_value _Coupling_constant_min_value _Coupling_constant_max_value _Coupling_constant_value_error 1 DHN 2 VAL H 2 VAL N 1.79 . . 0.1 2 DHN 3 ILE H 3 ILE N 2.64 . . 0.1 3 DHN 4 ASP H 4 ASP N 3.09 . . 0.1 4 DHN 5 THR H 5 THR N 4.26 . . 0.1 5 DHN 6 SER H 6 SER N 6.69 . . 0.1 6 DHN 7 ALA H 7 ALA N 7.29 . . 0.1 7 DHN 8 VAL H 8 VAL N 4.63 . . 0.1 8 DHN 9 GLU H 9 GLU N 8.18 . . 0.1 9 DHN 10 SER H 10 SER N 9.38 . . 0.1 10 DHN 11 ALA H 11 ALA N 6.98 . . 0.1 11 DHN 12 ILE H 12 ILE N 4.22 . . 0.1 12 DHN 13 THR H 13 THR N 7.44 . . 0.1 13 DHN 14 ASP H 14 ASP N 9.49 . . 0.1 14 DHN 17 GLY H 17 GLY N 8.67 . . 0.1 15 DHN 18 ASP H 18 ASP N 9.38 . . 0.1 16 DHN 19 MET H 19 MET N 5.01 . . 0.1 17 DHN 20 LYS H 20 LYS N 5.52 . . 0.1 18 DHN 21 ALA H 21 ALA N 9.22 . . 0.1 19 DHN 22 ILE H 22 ILE N 7.56 . . 0.1 20 DHN 23 GLY H 23 GLY N 4.92 . . 0.1 21 DHN 24 GLY H 24 GLY N 7.05 . . 0.1 22 DHN 25 TYR H 25 TYR N 8.99 . . 0.1 23 DHN 26 ILE H 26 ILE N 5.99 . . 0.1 24 DHN 27 VAL H 27 VAL N 5.63 . . 0.1 25 DHN 28 GLY H 28 GLY N 8.67 . . 0.1 26 DHN 29 ALA H 29 ALA N 7.64 . . 0.1 27 DHN 30 LEU H 30 LEU N 6.11 . . 0.1 28 DHN 31 VAL H 31 VAL N 4.62 . . 0.1 29 DHN 32 ILE H 32 ILE N 9.18 . . 0.1 30 DHN 33 LEU H 33 LEU N 8.12 . . 0.1 31 DHN 34 ALA H 34 ALA N 5.4 . . 0.1 32 DHN 35 VAL H 35 VAL N 6.6 . . 0.1 33 DHN 36 ALA H 36 ALA N 9.73 . . 0.1 34 DHN 37 GLY H 37 GLY N 7.81 . . 0.1 35 DHN 38 LEU H 38 LEU N 5.19 . . 0.1 36 DHN 39 ILE H 39 ILE N 9 . . 0.1 37 DHN 40 TYR H 40 TYR N 9.25 . . 0.1 38 DHN 41 SER H 41 SER N 6.21 . . 0.1 39 DHN 42 MET H 42 MET N 6.06 . . 0.1 40 DHN 43 LEU H 43 LEU N 9.7 . . 0.1 41 DHN 44 ARG H 44 ARG N 6.29 . . 0.1 42 DHN 45 LYS H 45 LYS N 1.56 . . 0.1 43 DHN 46 ALA H 46 ALA N 4.43 . . 0.1 stop_ save_