data_16400 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; SOLUTION STRUCTURE OF AN ABC COLLAGEN HETEROTRIMER REVEALS A SINGLE-REGISTER HELIX STABILIZED BY ELECTROSTATIC INTERACTIONS ; _BMRB_accession_number 16400 _BMRB_flat_file_name bmr16400.str _Entry_type new _Submission_date 2009-07-09 _Accession_date 2009-07-09 _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 Fallas Jorge A. . 2 Gauba Varun . . 3 Hartgerink Jeffrey D. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 3 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 46 "13C chemical shifts" 18 "15N chemical shifts" 5 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-05-28 update BMRB 'edit entity/assembly name' 2010-01-21 update BMRB 'complete entry citation' 2009-09-04 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Solution structure of an ABC collagen heterotrimer reveals a single-register helix stabilized by electrostatic interactions.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 19625247 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Fallas Jorge A. . 2 Gauba Varun . . 3 Hartgerink Jeffrey D. . stop_ _Journal_abbreviation 'J. Biol. Chem.' _Journal_name_full 'The Journal of biological chemistry' _Journal_volume 284 _Journal_issue 39 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 26851 _Page_last 26859 _Year 2009 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'ABC collagen heterotrimer' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'collagen A' $entity_1 'collagen B' $entity_2 'collagen C' $entity_3 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_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'collagen A' _Molecular_mass 2849.519 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 30 _Mol_residue_sequence ; PKGPKGPKGPKGPKGPKGPK GPKGPKGPKG ; loop_ _Residue_seq_code _Residue_label 1 PRO 2 LYS 3 GLY 4 PRO 5 LYS 6 GLY 7 PRO 8 LYS 9 GLY 10 PRO 11 LYS 12 GLY 13 PRO 14 LYS 15 GLY 16 PRO 17 LYS 18 GLY 19 PRO 20 LYS 21 GLY 22 PRO 23 LYS 24 GLY 25 PRO 26 LYS 27 GLY 28 PRO 29 LYS 30 GLY stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-06-23 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 PDB 2KLW "Solution Structure Of An Abc Collagen Heterotrimer Reveals A Single-Register Helix Stabilized By Electrostatic Interactions" 100.00 32 100.00 100.00 3.56e-04 stop_ save_ save_entity_2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'collagen B' _Molecular_mass 2868.582 _Mol_thiol_state 'not present' _Details . _Residue_count 30 _Mol_residue_sequence ; DXGDXGDXGDXGDXGDXGDX GDXGDXGDXG ; loop_ _Residue_seq_code _Residue_label 1 ASP 2 HYP 3 GLY 4 ASP 5 HYP 6 GLY 7 ASP 8 HYP 9 GLY 10 ASP 11 HYP 12 GLY 13 ASP 14 HYP 15 GLY 16 ASP 17 HYP 18 GLY 19 ASP 20 HYP 21 GLY 22 ASP 23 HYP 24 GLY 25 ASP 26 HYP 27 GLY 28 ASP 29 HYP 30 GLY stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_entity_3 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'collagen C' _Molecular_mass 2688.862 _Mol_thiol_state 'not present' _Details . _Residue_count 30 _Mol_residue_sequence ; PXGPXGPXGPXGPXGPXGPX GPXGPXGPXG ; loop_ _Residue_seq_code _Residue_label 1 PRO 2 HYP 3 GLY 4 PRO 5 HYP 6 GLY 7 PRO 8 HYP 9 GLY 10 PRO 11 HYP 12 GLY 13 PRO 14 HYP 15 GLY 16 PRO 17 HYP 18 GLY 19 PRO 20 HYP 21 GLY 22 PRO 23 HYP 24 GLY 25 PRO 26 HYP 27 GLY 28 PRO 29 HYP 30 GLY stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_HYP _Saveframe_category polymer_residue _Mol_type 'L-peptide linking' _Name_common 4-HYDROXYPROLINE _BMRB_code . _PDB_code HYP _Standard_residue_derivative . _Molecular_mass 131.130 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Tue Jun 9 14:36:58 2009 ; 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 . ? CD CD C . 0 . ? OD1 OD1 O . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG HG H . 0 . ? HD22 HD22 H . 0 . ? HD23 HD23 H . 0 . ? HD1 HD1 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 CD ? ? SING N H ? ? SING CA C ? ? SING CA CB ? ? SING CA HA ? ? DOUB C O ? ? SING C OXT ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG CD ? ? SING CG OD1 ? ? SING CG HG ? ? SING CD HD22 ? ? SING CD HD23 ? ? SING OD1 HD1 ? ? SING OXT HXT ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Details $entity_1 . . . . . . ; Synthetic Polymer following the (XYG)n motif of collagenous proteins ; $entity_2 . . . . . . ; Synthetic Polymer following the (XYG) motif of collagenous proteins ; $entity_3 . . . . . . ; Synthetic Polymer following the (XYG) motif of collagenous proteins ; 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 $entity_1 'chemical synthesis' . . . . . 'Fmoc based solid phase peptide synthesis' $entity_2 'chemical synthesis' . . . . . 'Fmoc based solid phase peptide synthesis' $entity_3 'chemical synthesis' . . . . . 'Fmoc based solid phase peptide 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 $entity_1 1.2 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_2 1.2 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_3 1.2 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ save_sample_4 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1.2 mM 'natural abundance' $entity_2 1.2 mM 'natural abundance' $entity_3 1.2 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ save_sample_5 _Saveframe_category sample _Sample_type solution _Details ; 10 mM phosphate buffer Not all amino acids labeled, refer to publication for sequence ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1.2 mM '[U-99% 13C; U-99% 15N]' $entity_2 1.2 mM '[U-99% 13C; U-99% 15N]' $entity_3 1.2 mM '[U-99% 13C; U-99% 15N]' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' 'phosphate buffer' 10 mM 'natural abundance' stop_ save_ save_sample_6 _Saveframe_category sample _Sample_type solution _Details ; 10 mM phosphate buffer Not all amino acids labeled, refer to publication for sequence ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1.8 mM 'natural abundance' $entity_2 1.2 mM 'natural abundance' $entity_3 1.2 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' 'phosphate buffer' 10 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CNS _Saveframe_category software _Name CNS _Version 'v 1.21' loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_AMBER _Saveframe_category software _Name AMBER _Version 9 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_CcpNMR _Saveframe_category software _Name CcpNMR _Version . loop_ _Vendor _Address _Electronic_address CCPN . . stop_ loop_ _Task 'data analysis' 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_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 800 _Details 'equipped with a cold probe' save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_4 save_ save_2D_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_4 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_TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_2 save_ save_2D_1H-1H_TOCSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_3 save_ save_2D_1H-1H_NOESY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_3 save_ save_2D_1H-13C_HSQC_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_5 save_ save_2D_1H-15N_HSQC_8 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_5 save_ save_3D_HNHA_9 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNHA' _Sample_label $sample_5 save_ save_2D_1H-1H_13C-HMQC_NOESY_15N-HSQC_10 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H 13C-HMQC NOESY 15N-HSQC' _Sample_label $sample_5 save_ save_2D_1H-1H_NOESY_11 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_4 save_ save_2D_1H-1H_TOCSY_12 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_4 save_ save_2D_1H-15N_HSQC_13 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_6 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 . K pH 7 . 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 283 . K pH 7 . 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 TSP H 1 'methyl protons' ppm 0 internal direct . . . 1.0 TSP C 13 'methyl carbon' ppm 0 internal direct . . . 1.0 'Internal Standard (POG10)' N 15 nitrogen ppm 106.6 internal direct . . . 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_assigned_chem_shift_list_1_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H TOCSY' '2D 1H-1H NOESY' '2D 1H-13C HSQC' '2D 1H-15N HSQC' stop_ loop_ _Sample_label $sample_4 $sample_5 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'collagen A' _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 5 4 PRO HA H 4.465 0.005 1 2 5 4 PRO HB2 H 2.283 0.005 1 3 5 4 PRO HB3 H 1.903 0.005 1 4 5 4 PRO HD2 H 3.252 0.005 1 5 5 4 PRO HD3 H 3.562 0.005 1 6 5 4 PRO HG2 H 1.958 0.005 2 7 5 4 PRO HG3 H 1.958 0.005 2 8 5 4 PRO CA C 62.243 0.020 1 9 5 4 PRO CB C 32.518 0.020 1 10 5 4 PRO CD C 49.733 0.020 1 11 5 4 PRO CG C 27.833 0.020 1 12 6 5 LYS H H 8.325 0.005 1 13 6 5 LYS HA H 4.349 0.005 1 14 6 5 LYS HB2 H 1.654 0.005 1 15 6 5 LYS HB3 H 1.828 0.005 1 16 6 5 LYS HD2 H 1.701 0.005 2 17 6 5 LYS HD3 H 1.701 0.005 2 18 6 5 LYS HE2 H 3.068 0.005 2 19 6 5 LYS HE3 H 3.068 0.005 2 20 6 5 LYS HG2 H 1.675 0.005 1 21 6 5 LYS HG3 H 1.283 0.005 1 22 6 5 LYS CA C 56.872 0.020 1 23 6 5 LYS CB C 33.175 0.020 1 24 6 5 LYS CD C 30.236 0.020 1 25 6 5 LYS CE C 42.600 0.020 1 26 6 5 LYS CG C 25.136 0.020 1 27 6 5 LYS N N 124.000 0.010 1 28 7 6 GLY H H 8.347 0.005 1 29 7 6 GLY HA2 H 3.752 0.005 1 30 7 6 GLY HA3 H 3.860 0.005 1 31 7 6 GLY CA C 45.636 0.020 1 32 7 6 GLY N N 110.356 0.010 1 stop_ save_ save_assigned_chem_shift_list_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H TOCSY' '2D 1H-1H NOESY' '2D 1H-13C HSQC' '2D 1H-15N HSQC' stop_ loop_ _Sample_label $sample_4 $sample_5 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'collagen B' _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 37 4 ASP CA C 53.344 0.020 1 2 37 4 ASP CB C 39.264 0.020 1 3 37 4 ASP H H 8.699 0.005 1 4 37 4 ASP HA H 4.735 0.005 1 5 37 4 ASP HB2 H 2.766 0.005 1 6 37 4 ASP HB3 H 2.233 0.005 1 7 37 4 ASP N N 118.800 0.010 1 8 38 5 HYP HA H 4.686 0.005 1 9 38 5 HYP HB2 H 2.007 0.005 1 10 38 5 HYP HB3 H 2.209 0.005 1 11 38 5 HYP HD22 H 3.743 0.005 1 12 38 5 HYP HD23 H 3.859 0.005 1 13 38 5 HYP HG H 4.645 0.005 1 14 39 6 GLY CA C 44.929 0.020 1 15 39 6 GLY H H 8.061 0.005 1 16 39 6 GLY HA2 H 3.635 0.005 1 17 39 6 GLY HA3 H 3.706 0.005 1 18 39 6 GLY N N 105.616 0.010 1 stop_ save_ save_assigned_chem_shift_list_1_3 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H TOCSY' '2D 1H-1H NOESY' '2D 1H-13C HSQC' '2D 1H-15N HSQC' stop_ loop_ _Sample_label $sample_4 $sample_5 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'collagen C' _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 69 4 PRO CA C 61.427 0.020 1 2 69 4 PRO CB C 30.606 0.020 1 3 69 4 PRO CD C 50.055 0.020 1 4 69 4 PRO CG C 27.031 0.020 1 5 69 4 PRO HA H 4.765 0.005 1 6 69 4 PRO HB2 H 2.283 0.005 1 7 69 4 PRO HB3 H 2.109 0.005 1 8 69 4 PRO HD2 H 3.201 0.005 1 9 69 4 PRO HD3 H 3.555 0.005 1 10 69 4 PRO HG2 H 1.996 0.005 2 11 69 4 PRO HG3 H 1.996 0.005 2 12 70 5 HYP HA H 4.830 0.005 1 13 70 5 HYP HB2 H 2.103 0.005 1 14 70 5 HYP HB3 H 2.203 0.005 1 15 71 6 GLY CA C 45.013 0.020 1 16 71 6 GLY H H 8.264 0.005 1 17 71 6 GLY HA2 H 3.535 0.005 1 18 71 6 GLY HA3 H 3.859 0.005 1 19 71 6 GLY N N 107.891 0.010 1 stop_ save_