data_11521 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; The chemical shift assignments of the headpiece subdomain of chicken villin protein under the crowded condition with the segment B1 of streptococcal protein G ; _BMRB_accession_number 11521 _BMRB_flat_file_name bmr11521.str _Entry_type original _Submission_date 2012-12-13 _Accession_date 2012-12-14 _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 Tochio Naoya . . 2 Kigawa Takanori . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 33 "15N chemical shifts" 33 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-02-15 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 11519 'The chemical shift assignments of the headpiece subdomain of chicken villin protein under the diluted condition' 11520 'The chemical shift assignments of the headpiece subdomain of chicken villin protein under the crowded condition' stop_ _Original_release_date 2013-02-15 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Reduced native state stability in crowded cellular environment due to protein-protein interactions' _Citation_status 'in preparation' _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Harada Ryuhei . . 2 Tochio Naoya . . 3 Kigawa Takanori . . 4 Sugita Yuji . . 5 Feig Michael . . stop_ _Journal_abbreviation 'Not known' _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name Villin _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label Villin $protein 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_protein _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common protein _Molecular_mass . _Mol_thiol_state 'all free' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 36 _Mol_residue_sequence ; MLSDEDFKAVFGMTRSAFAN LPLWKQQNLKKEKGLF ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 MET 2 2 LEU 3 3 SER 4 4 ASP 5 5 GLU 6 6 ASP 7 7 PHE 8 8 LYS 9 9 ALA 10 10 VAL 11 11 PHE 12 12 GLY 13 13 MET 14 14 THR 15 15 ARG 16 16 SER 17 17 ALA 18 18 PHE 19 19 ALA 20 20 ASN 21 21 LEU 22 22 PRO 23 23 LEU 24 24 TRP 25 25 LYS 26 26 GLN 27 27 GLN 28 28 ASN 29 29 LEU 30 30 LYS 31 31 LYS 32 32 GLU 33 33 LYS 34 34 GLY 35 35 LEU 36 36 PHE 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 11519 protein 100.00 36 100.00 100.00 2.57e-16 BMRB 11520 protein 100.00 36 100.00 100.00 2.57e-16 BMRB 15097 D6-HP 97.22 208 100.00 100.00 1.77e-14 BMRB 15245 villin_G34L 100.00 36 97.22 97.22 5.60e-15 BMRB 17698 HP67_H41F 97.22 67 100.00 100.00 1.85e-15 BMRB 19911 VILLIN-1 66.67 26 100.00 100.00 3.49e-07 BMRB 4428 "HEADPIECE DOMAIN FROM CHICKEN VILLIN" 97.22 67 100.00 100.00 1.46e-15 PDB 1QQV "Solution Structure Of The Headpiece Domain Of Chicken Villin" 97.22 67 100.00 100.00 1.46e-15 PDB 1VII "Thermostable Subdomain From Chicken Villin Headpiece, Nmr, Minimized Average Structure" 100.00 36 100.00 100.00 2.57e-16 PDB 1YRF "Chicken Villin Subdomain Hp-35, N68h, Ph6.7" 97.22 35 97.14 100.00 6.36e-15 PDB 1YRI "Chicken Villin Subdomain Hp-35, N68h, Ph6.4" 97.22 35 97.14 100.00 6.36e-15 PDB 1YU5 "Crystal Structure Of The Headpiece Domain Of Chicken Villin" 97.22 67 100.00 100.00 1.46e-15 PDB 1YU7 "Crystal Structure Of The W64y Mutant Of Villin Headpiece" 97.22 67 97.14 100.00 6.28e-15 PDB 1YU8 "Crystal Structure Of The R37a Mutant Of Villin Headpiece" 97.22 67 100.00 100.00 1.40e-15 PDB 2PPZ "Nmr Solution Structure Of The Villin Headpiece Mutant G34l" 100.00 36 97.22 97.22 5.60e-15 PDB 2RJV "Crystal Structure Of The H41y Mutant Of Villin Headpiece, P 21 21 21 Space Group" 97.22 67 100.00 100.00 1.44e-15 PDB 2RJW "The Crystal Structure Of The H41y Mutant Of Villin Headpiece, P61 Space Group" 97.22 67 100.00 100.00 1.44e-15 PDB 2RJX "Crystal Structure Of The Headpiece Domain Of Chicken Villin, P61 Space Group" 97.22 67 100.00 100.00 1.46e-15 PDB 2RJY "Crystal Structure Of Villin Headpiece, P21 21 21 Space Group" 97.22 67 100.00 100.00 1.46e-15 PDB 3MYA "Crystal Structure Of Hp67 H41f - P61" 97.22 67 100.00 100.00 1.85e-15 PDB 3MYC "Crystal Structure Of Hp67 H41f - P212121" 97.22 67 100.00 100.00 1.85e-15 PDB 3MYE "Crystal Structure Of Hp67 L61gl" 100.00 68 97.22 97.22 9.96e-14 PDB 3NKJ "Crystal Structure Of Hp67 L61g" 97.22 67 97.14 97.14 1.96e-14 PDB 4CZ3 "Hp24wt Derived From The Villin Headpiece Subdomain" 66.67 26 100.00 100.00 3.49e-07 GB AAA49133 "villin [Gallus gallus]" 97.22 826 100.00 100.00 7.10e-14 REF NP_990773 "villin-1 [Gallus gallus]" 97.22 826 100.00 100.00 7.10e-14 REF XP_003207697 "PREDICTED: villin-1 [Meleagris gallopavo]" 97.22 826 100.00 100.00 6.90e-14 REF XP_010711916 "PREDICTED: villin-1 [Meleagris gallopavo]" 97.22 826 100.00 100.00 6.90e-14 REF XP_010711917 "PREDICTED: villin-1 [Meleagris gallopavo]" 97.22 826 100.00 100.00 6.90e-14 SP P02640 "RecName: Full=Villin-1" 97.22 826 100.00 100.00 7.10e-14 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $protein chicken 9031 Eukaryota Metazoa Gallus gallus 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 $protein 'recombinant technology' 'E. coli' Escherichia coli . P120522-02 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 $protein 1 mM [U-15N] HEPES 50 mM 'natural abundance' 'protein G' 16 mM 'natural abundance' D2O 10 % . H2O 90 % . stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection 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_NMRView _Saveframe_category software _Name NMRView _Version . loop_ _Vendor _Address _Electronic_address 'Johnson, One Moon Scientific' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_KUJIRA _Saveframe_category software _Name Kujira _Version . loop_ _Vendor _Address _Electronic_address 'N. Kobayashi' . . 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 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_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 0 . mM pH 7.0 . pH pressure 1 . atm temperature 298 . 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 water H 1 protons ppm 4.784 internal direct . . . 1 water N 15 protons ppm 4.784 internal 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' 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 Villin _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 3 3 SER H H 9.596 0.030 1 2 3 3 SER N N 121.142 0.300 1 3 4 4 ASP H H 9.136 0.030 1 4 4 4 ASP N N 122.344 0.300 1 5 5 5 GLU H H 8.793 0.030 1 6 5 5 GLU N N 119.777 0.300 1 7 6 6 ASP H H 7.998 0.030 1 8 6 6 ASP N N 122.618 0.300 1 9 7 7 PHE H H 9.026 0.030 1 10 7 7 PHE N N 121.683 0.300 1 11 8 8 LYS H H 7.882 0.030 1 12 8 8 LYS N N 118.675 0.300 1 13 9 9 ALA H H 7.688 0.030 1 14 9 9 ALA N N 122.113 0.300 1 15 10 10 VAL H H 7.868 0.030 1 16 10 10 VAL N N 117.178 0.300 1 17 11 11 PHE H H 8.476 0.030 1 18 11 11 PHE N N 113.600 0.300 1 19 12 12 GLY H H 8.179 0.030 1 20 12 12 GLY N N 108.503 0.300 1 21 13 13 MET H H 7.594 0.030 1 22 13 13 MET N N 113.909 0.300 1 23 14 14 THR H H 8.192 0.030 1 24 14 14 THR N N 107.444 0.300 1 25 15 15 ARG H H 8.778 0.030 1 26 15 15 ARG N N 120.877 0.300 1 27 16 16 SER H H 8.200 0.030 1 28 16 16 SER N N 113.772 0.300 1 29 17 17 ALA H H 7.626 0.030 1 30 17 17 ALA N N 125.182 0.300 1 31 18 18 PHE H H 8.439 0.030 1 32 18 18 PHE N N 121.541 0.300 1 33 19 19 ALA H H 7.835 0.030 1 34 19 19 ALA N N 117.649 0.300 1 35 20 20 ASN H H 7.207 0.030 1 36 20 20 ASN N N 113.556 0.300 1 37 21 21 LEU H H 7.403 0.030 1 38 21 21 LEU N N 121.846 0.300 1 39 23 23 LEU H H 8.930 0.030 1 40 23 23 LEU N N 124.946 0.300 1 41 24 24 TRP H H 8.045 0.030 1 42 24 24 TRP N N 115.085 0.300 1 43 25 25 LYS H H 6.058 0.030 1 44 25 25 LYS N N 123.777 0.300 1 45 26 26 GLN H H 7.627 0.030 1 46 26 26 GLN N N 118.935 0.300 1 47 27 27 GLN H H 8.218 0.030 1 48 27 27 GLN N N 115.508 0.300 1 49 28 28 ASN H H 7.946 0.030 1 50 28 28 ASN N N 119.272 0.300 1 51 29 29 LEU H H 8.430 0.030 1 52 29 29 LEU N N 121.305 0.300 1 53 30 30 LYS H H 8.250 0.030 1 54 30 30 LYS N N 118.123 0.300 1 55 31 31 LYS H H 8.047 0.030 1 56 31 31 LYS N N 119.111 0.300 1 57 32 32 GLU H H 8.294 0.030 1 58 32 32 GLU N N 119.949 0.300 1 59 33 33 LYS H H 7.828 0.030 1 60 33 33 LYS N N 114.826 0.300 1 61 34 34 GLY H H 7.856 0.030 1 62 34 34 GLY N N 107.106 0.300 1 63 35 35 LEU H H 7.819 0.030 1 64 35 35 LEU N N 120.482 0.300 1 65 36 36 PHE H H 7.579 0.030 1 66 36 36 PHE N N 123.837 0.300 1 stop_ save_