data_17413 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; B. ste. A26I Holo TRAP Ile, Leu, and Val methyls ; _BMRB_accession_number 17413 _BMRB_flat_file_name bmr17413.str _Entry_type original _Submission_date 2011-01-17 _Accession_date 2011-01-17 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'B. ste. A26I holo TRAP. 1H,13C-HSQC NMR spectra at 25C, 800 MHz, with stereo-assigned chemical shifts for methyl groups on Ile, Leu, and Val side chains' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Kleckner Ian R. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 29 "13C chemical shifts" 29 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-02-13 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 17400 'protein of apo form' stop_ _Original_release_date 2012-02-13 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Mechanisms of allosteric gene regulation by NMR quantification of microsecond-millisecond protein dynamics' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 22115774 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Kleckner Ian R. . 2 Gollnick Paul . . 3 Foster Mark P. . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_volume 415 _Journal_issue 2 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 372 _Page_last 381 _Year 2012 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name TRAP11 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'TRAP, chain 1' $TRAP 'TRAP, chain 2' $TRAP 'TRAP, chain 3' $TRAP 'TRAP, chain 4' $TRAP 'TRAP, chain 5' $TRAP 'TRAP, chain 6' $TRAP 'TRAP, chain 7' $TRAP 'TRAP, chain 8' $TRAP 'TRAP, chain 9' $TRAP 'TRAP, chain 10' $TRAP 'TRAP, chain 11' $TRAP L-tryptophan $TRP stop_ _System_molecular_weight 91128 _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details 'TRAP primarily exists as a homo-11mer in solution' save_ ######################## # Monomeric polymers # ######################## save_TRAP _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common TRAP _Molecular_mass . _Mol_thiol_state 'not present' loop_ _Biological_function 'Binds tryptophan ligand and only then is activated to bind trp-RNA' stop_ _Details 'Exists as ring-shaped homo-11mer in solution' ############################## # Polymer residue sequence # ############################## _Residue_count 74 _Mol_residue_sequence ; MYTNSDFVVIKALEDGVNVI GLTRGIDTRFHHSEKLDKGE VLIAQFTEHTSAIKVRGKAY IQTRHGVIESEGKK ; loop_ _Residue_seq_code _Residue_label 1 MET 2 TYR 3 THR 4 ASN 5 SER 6 ASP 7 PHE 8 VAL 9 VAL 10 ILE 11 LYS 12 ALA 13 LEU 14 GLU 15 ASP 16 GLY 17 VAL 18 ASN 19 VAL 20 ILE 21 GLY 22 LEU 23 THR 24 ARG 25 GLY 26 ILE 27 ASP 28 THR 29 ARG 30 PHE 31 HIS 32 HIS 33 SER 34 GLU 35 LYS 36 LEU 37 ASP 38 LYS 39 GLY 40 GLU 41 VAL 42 LEU 43 ILE 44 ALA 45 GLN 46 PHE 47 THR 48 GLU 49 HIS 50 THR 51 SER 52 ALA 53 ILE 54 LYS 55 VAL 56 ARG 57 GLY 58 LYS 59 ALA 60 TYR 61 ILE 62 GLN 63 THR 64 ARG 65 HIS 66 GLY 67 VAL 68 ILE 69 GLU 70 SER 71 GLU 72 GLY 73 LYS 74 LYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-07-15 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 17400 TRAP 100.00 74 100.00 100.00 1.14e-44 PDB 1C9S "Crystal Structure Of A Complex Of Trp Rna-Binding Attenuation Protein With A 53-Base Single Stranded Rna Containing Eleven Gag " 100.00 74 98.65 98.65 5.53e-44 PDB 1GTF "The Structure Of The Trp Rna-Binding Attenuation Protein (Trap) Bound To A 53-Nucleotide Rna Molecule Containing Gaguu Repeats" 100.00 74 98.65 98.65 5.53e-44 PDB 1GTN "Structure Of The Trp Rna-binding Attenuation Protein (trap) Bound To An Rna Molecule Containing 11 Gagcc Repeats" 100.00 74 98.65 98.65 5.53e-44 PDB 1QAW "Regulatory Features Of The Trp Operon And The Crystal Structure Of The Trp Rna-Binding Attenuation Protein From Bacillus Stearo" 100.00 74 98.65 98.65 5.53e-44 PDB 1UTD "The Structure Of The Trp Rna-binding Attenuation Protein (trap) Bound To A 63-nucleotide Rna Molecule Containing Gaguuu Repeats" 100.00 74 98.65 98.65 5.53e-44 PDB 1UTF "The Structure Of The Trp Rna-Binding Attenuation Protein (Trap) Bound To A Rna Molecule Containing Uagau Repeats (Part I)" 100.00 74 98.65 98.65 5.53e-44 PDB 1UTV "The Structure Of The Trp Rna-Binding Attenuation Protein (Trap) Bound To A Rna Molecule Containing Uagau Repeats (Part Ii)" 100.00 74 98.65 98.65 5.53e-44 PDB 2EXS "Trap3 (Engineered Trap)" 98.65 77 97.26 97.26 3.22e-42 PDB 2EXT "Trap4 (Engineered Trap)" 98.65 77 98.63 98.63 3.14e-43 PDB 2ZCZ "Crytal Structures And Thermostability Of Mutant Trap3 A7 (Engineered Trap)" 100.00 81 98.65 98.65 1.49e-44 PDB 2ZD0 "Crytal Structures And Thermostability Of Mutant Trap3 A5 (Engineered Trap)" 100.00 79 98.65 98.65 2.38e-44 PDB 2ZP8 "The Nature Of The Trap:anti-trap Complex" 100.00 74 98.65 98.65 5.53e-44 PDB 2ZP9 "The Nature Of The Trap:anti-trap Complex" 100.00 81 98.65 98.65 1.49e-44 PDB 3AQD "Unliganded Trap" 100.00 74 98.65 98.65 5.53e-44 PDB 3ZZS "Engineered 12-Subunit Bacillus Stearothermophilus Trp Rna-Binding Attenuation Protein (Trap)" 87.84 65 98.46 98.46 1.60e-36 DBJ BAD76498 "transcription attenuation protein (tryptophan RNA-binding attenuator protein) (trp RNA-binding attenuation protein) [Geobacillu" 100.00 74 97.30 98.65 1.02e-43 DBJ GAD12442 "mutant Trap3 A7 [Geobacillus kaustophilus GBlys]" 100.00 74 97.30 98.65 1.02e-43 DBJ GAJ58441 "transcription attenuation protein MtrB [Geobacillus thermoleovorans B23]" 100.00 74 97.30 98.65 1.02e-43 GB AAD33793 "trp RNA-binding attenuation protein [Geobacillus stearothermophilus]" 100.00 74 98.65 98.65 5.53e-44 GB ABO67499 "Trp RNA-binding attenuation protein [Geobacillus thermodenitrificans NG80-2]" 100.00 75 97.30 97.30 1.78e-43 GB ACX77149 "tryptophan RNA-binding attenuator protein [Geobacillus sp. Y412MC61]" 100.00 74 97.30 98.65 1.02e-43 GB ADI26315 "tryptophan RNA-binding attenuator protein [Geobacillus sp. C56-T3]" 100.00 74 97.30 98.65 1.02e-43 GB ADU94597 "tryptophan RNA-binding attenuator protein [Geobacillus sp. Y412MC52]" 100.00 74 97.30 98.65 1.02e-43 REF WP_008879621 "MULTISPECIES: tryptophan RNA-binding attenuator protein [Bacillaceae]" 100.00 74 97.30 97.30 1.91e-43 REF WP_011231698 "MULTISPECIES: transcription attenuation protein MtrB [Geobacillus]" 100.00 74 97.30 98.65 1.02e-43 REF WP_033013997 "MULTISPECIES: transcription attenuation protein MtrB [Geobacillus]" 100.00 74 98.65 98.65 5.53e-44 SP Q9X6J6 "RecName: Full=Transcription attenuation protein MtrB; AltName: Full=Trp RNA-binding attenuation protein; Short=TRAP; AltName: F" 100.00 74 98.65 98.65 5.53e-44 stop_ save_ ############# # Ligands # ############# save_TRP _Saveframe_category ligand _Mol_type "non-polymer (L-peptide linking)" _Name_common "TRP (TRYPTOPHAN)" _BMRB_code . _PDB_code TRP _Molecular_mass 204.225 _Mol_charge 0 _Mol_paramagnetic no _Mol_aromatic yes _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Thu Jan 20 13:51:36 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? CA CA C . 0 . ? C C C . 0 . ? O O O . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? CD1 CD1 C . 0 . ? CD2 CD2 C . 0 . ? NE1 NE1 N . 0 . ? CE2 CE2 C . 0 . ? CE3 CE3 C . 0 . ? CZ2 CZ2 C . 0 . ? CZ3 CZ3 C . 0 . ? CH2 CH2 C . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HD1 HD1 H . 0 . ? HE1 HE1 H . 0 . ? HE3 HE3 H . 0 . ? HZ2 HZ2 H . 0 . ? HZ3 HZ3 H . 0 . ? HH2 HH2 H . 0 . ? HXT HXT 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 SING N CA ? ? SING N H ? ? SING N H2 ? ? SING CA C ? ? SING CA CB ? ? SING CA HA ? ? DOUB C O ? ? SING C OXT ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? DOUB CG CD1 ? ? SING CG CD2 ? ? SING CD1 NE1 ? ? SING CD1 HD1 ? ? DOUB CD2 CE2 ? ? SING CD2 CE3 ? ? SING NE1 CE2 ? ? SING NE1 HE1 ? ? SING CE2 CZ2 ? ? DOUB CE3 CZ3 ? ? SING CE3 HE3 ? ? DOUB CZ2 CH2 ? ? SING CZ2 HZ2 ? ? SING CZ3 CH2 ? ? SING CZ3 HZ3 ? ? SING CH2 HH2 ? ? SING OXT HXT ? ? 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 $TRAP 'Bacillus stearothermophilus' 1422 Eubacteria . Bacillus stearothermophilus 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 $TRAP 'recombinant technology' . Escherichia coli . pET32 'Not sure if vector is accurate' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_A26I-TRAP-ILV _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $TRAP 1-1.5 mM '[U-2H; U-15N; ILV-(13CH3)]' 'potassium chloride' 50 mM 'natural abundance' 'sodium chloride' 100 mM 'natural abundance' 'sodium azide' 0.02 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-13C_HSQC_aliphatic_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aliphatic' _Sample_label $A26I-TRAP-ILV save_ ####################### # Sample conditions # ####################### save_25C _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 8.0 . pH pressure 1 . atm temperature 273 . 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 0.00 . indirect . 'separate tube (no insert) similar to the experimental sample tube' . 0.251449530 DSS H 1 'methyl protons' ppm 0.00 internal direct . 'separate tube (no insert) similar to the experimental sample tube' . 1.000000000 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-13C HSQC aliphatic' stop_ loop_ _Sample_label $A26I-TRAP-ILV stop_ _Sample_conditions_label $25C _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'TRAP, chain 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 8 8 VAL HG1 H 0.4819 0.0115 1 2 8 8 VAL HG2 H 0.5491 0.0115 1 3 8 8 VAL CG1 C 21.3903 0.0815 1 4 8 8 VAL CG2 C 19.0018 0.0815 1 5 9 9 VAL HG1 H 0.8833 0.0115 1 6 9 9 VAL HG2 H 1.2028 0.0115 1 7 9 9 VAL CG1 C 21.5026 0.0815 1 8 9 9 VAL CG2 C 21.6306 0.0815 1 9 10 10 ILE HD1 H 0.6526 0.0115 1 10 10 10 ILE CD1 C 16.0591 0.0815 1 11 13 13 LEU HD1 H 0.9051 0.0115 1 12 13 13 LEU HD2 H 0.8077 0.0115 1 13 13 13 LEU CD1 C 25.5734 0.0815 1 14 13 13 LEU CD2 C 21.3581 0.0815 1 15 17 17 VAL HG1 H 0.6500 0.0115 1 16 17 17 VAL HG2 H 1.1048 0.0115 1 17 17 17 VAL CG1 C 20.4585 0.0815 1 18 17 17 VAL CG2 C 24.5672 0.0815 1 19 19 19 VAL HG1 H 0.6264 0.0115 1 20 19 19 VAL HG2 H 0.7879 0.0115 1 21 19 19 VAL CG1 C 21.0844 0.0815 1 22 19 19 VAL CG2 C 21.4318 0.0815 1 23 20 20 ILE HD1 H 0.4678 0.0115 1 24 20 20 ILE CD1 C 14.0488 0.0815 1 25 22 22 LEU HD1 H 0.4948 0.0115 1 26 22 22 LEU HD2 H 0.5218 0.0115 1 27 22 22 LEU CD1 C 24.2319 0.0815 1 28 22 22 LEU CD2 C 24.6889 0.0815 1 29 26 26 ILE HD1 H 0.8190 0.0115 1 30 26 26 ILE CD1 C 13.7874 0.0815 1 31 36 36 LEU HD1 H 0.7346 0.0115 1 32 36 36 LEU HD2 H 0.7778 0.0115 1 33 36 36 LEU CD1 C 25.8037 0.0815 1 34 36 36 LEU CD2 C 24.3787 0.0815 1 35 41 41 VAL HG1 H 0.7079 0.0115 1 36 41 41 VAL HG2 H 0.7874 0.0115 1 37 41 41 VAL CG1 C 21.2028 0.0815 1 38 41 41 VAL CG2 C 21.9008 0.0815 1 39 42 42 LEU HD1 H 0.5819 0.0115 1 40 42 42 LEU HD2 H 0.4115 0.0115 1 41 42 42 LEU CD1 C 23.2970 0.0815 1 42 42 42 LEU CD2 C 26.0846 0.0815 1 43 43 43 ILE HD1 H 0.6539 0.0115 1 44 43 43 ILE CD1 C 14.4717 0.0815 1 45 53 53 ILE HD1 H 0.1903 0.0115 1 46 53 53 ILE CD1 C 13.1484 0.0815 1 47 55 55 VAL HG1 H 0.7266 0.0115 1 48 55 55 VAL HG2 H 0.7293 0.0115 1 49 55 55 VAL CG1 C 21.6525 0.0815 1 50 55 55 VAL CG2 C 21.0219 0.0815 1 51 61 61 ILE HD1 H 0.7260 0.0115 1 52 61 61 ILE CD1 C 14.5725 0.0815 1 53 67 67 VAL HG1 H 0.7079 0.0115 1 54 67 67 VAL HG2 H 0.8413 0.0115 1 55 67 67 VAL CG1 C 21.2028 0.0815 1 56 67 67 VAL CG2 C 20.9014 0.0815 1 57 68 68 ILE HD1 H 0.8392 0.0115 1 58 68 68 ILE CD1 C 15.3697 0.0815 1 stop_ save_