data_4066 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Amplification of One-Bond 1H/2H Isotope Efects on 15N Chemical Shifts in Clostridium pasteurianum Rubredoxin by Fermi-Contact Effects through Hydrogen Bonds --Fe(III) ; _BMRB_accession_number 4066 _BMRB_flat_file_name bmr4066.str _Entry_type original _Submission_date 1998-04-22 _Accession_date 1998-04-22 _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 Xia Bin . . 2 Wilkens Steven J. . 3 Westler William M. . 4 Markley John L. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "15N chemical shifts" 8 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 1998-06-18 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 4050 '1H, 13C, and 15N chemical shifts for reduced rubredoxin' 4051 '1H, 13C, and 15N chemical shifts for oxidized rubredoxin' 4137 'reduced form' stop_ _Original_release_date 1998-06-18 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full ; Xia, B., Wilkens, S.J., Westler, W.M., Markley, J.L., "Amplification of One-Bond 1H/2H Isotope Efects on 15N Chemical Shifts in Clostridium pasteurianum Rubredoxin by Fermi-Contact Effects through Hydrogen Bonds," J. Am. Chem. Soc. 120, 4893-4894 (1998). ; _Citation_title ; Amplification of One-Bond 1H/2H Isotope Efects on 15N Chemical Shifts in Clostridium pasteurianum Rubredoxin by Fermi-Contact Effects through Hydrogen Bonds ; _Citation_status published _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 Xia Bin . . 2 Wilkens Steven J. . 3 Westler William M. . 4 Markley John L. . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_volume 120 _Journal_issue 19 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 4893 _Page_last 4894 _Year 1998 _Details . loop_ _Keyword 'iron-sulfur center' 'isotope effect' NMR protein 'rubredoxin oxidized' stop_ save_ ####################################### # Cited references within the entry # ####################################### save_citation_one _Saveframe_category citation _Citation_full ; Xia, B., Westler, W.M., Cheng, H., Moulis, J.-M., and Markley, J.L. J. Am. Chem. Soc. 117, 5347 (1995). ; _Citation_title . _Citation_status . _Citation_type . _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? _Journal_abbreviation . _Journal_name_full . _Journal_volume . _Journal_issue . _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first . _Page_last . _Year . _Details . save_ ################################## # Molecular system description # ################################## save_system_RdxIII _Saveframe_category molecular_system _Mol_system_name rubredoxin _Abbreviation_common Rdx _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label RdxIII $RdxIII Fe(III) $FE stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic yes _System_thiol_state . loop_ _Biological_function ; Rubredoxin is a component of the electron transport system and its function is undetermined ; stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_RdxIII _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common rubredoxin _Abbreviation_common Rdx _Molecular_mass . _Mol_thiol_state . _Details 'oxidized form' ############################## # Polymer residue sequence # ############################## _Residue_count 54 _Mol_residue_sequence ; MKKYTCTVCGYIYNPEDGDP DNGVNPGTDFKDIPDDWVCP LCGVGKDQFEEVEE ; loop_ _Residue_seq_code _Residue_label 1 MET 2 LYS 3 LYS 4 TYR 5 THR 6 CYS 7 THR 8 VAL 9 CYS 10 GLY 11 TYR 12 ILE 13 TYR 14 ASN 15 PRO 16 GLU 17 ASP 18 GLY 19 ASP 20 PRO 21 ASP 22 ASN 23 GLY 24 VAL 25 ASN 26 PRO 27 GLY 28 THR 29 ASP 30 PHE 31 LYS 32 ASP 33 ILE 34 PRO 35 ASP 36 ASP 37 TRP 38 VAL 39 CYS 40 PRO 41 LEU 42 CYS 43 GLY 44 VAL 45 GLY 46 LYS 47 ASP 48 GLN 49 PHE 50 GLU 51 GLU 52 VAL 53 GLU 54 GLU stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-10-13 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 4050 "rubredoxin peptide" 100.00 54 100.00 100.00 6.32e-30 BMRB 4051 "rubredoxin peptide" 100.00 54 100.00 100.00 6.32e-30 BMRB 4137 rubredoxin 100.00 54 100.00 100.00 6.32e-30 BMRB 4182 "reduced rubredoxin" 100.00 54 100.00 100.00 6.32e-30 BMRB 4319 "rubredoxin peptide" 100.00 54 100.00 100.00 6.32e-30 BMRB 4320 "rubredoxin peptide" 100.00 54 100.00 100.00 6.32e-30 PDB 1B13 "Clostridium Pasteurianum Rubredoxin G10a Mutant" 100.00 54 98.15 98.15 1.91e-29 PDB 1B2J "Clostridium Pasteurianum Rubredoxin G43a Mutant" 100.00 54 98.15 98.15 1.91e-29 PDB 1BE7 "Clostridium Pasteurianum Rubredoxin C42s Mutant" 100.00 54 98.15 98.15 4.65e-29 PDB 1BFY "Solution Structure Of Reduced Clostridium Pasteurianum Rubredoxin, Nmr, 20 Structures" 98.15 54 100.00 100.00 6.80e-29 PDB 1C09 "Rubredoxin V44a Cp" 100.00 54 98.15 98.15 1.54e-29 PDB 1FHH "X-Ray Crystal Structure Of Oxidized Rubredoxin" 100.00 54 100.00 100.00 6.32e-30 PDB 1FHM "X-Ray Crystal Structure Of Reduced Rubredoxin" 100.00 54 100.00 100.00 6.32e-30 PDB 1IRN "Rubredoxin (zn-substituted) At 1.2 Angstroms Resolution" 100.00 54 100.00 100.00 6.32e-30 PDB 1IRO "Rubredoxin (Oxidized, Fe(Iii)) At 1.1 Angstroms Resolution" 100.00 54 100.00 100.00 6.32e-30 PDB 1R0F "Gallium-Substituted Rubredoxin" 100.00 54 100.00 100.00 6.32e-30 PDB 1R0G "Mercury-Substituted Rubredoxin" 100.00 54 100.00 100.00 6.32e-30 PDB 1R0H "Cobalt-Substituted Rubredoxin" 100.00 54 100.00 100.00 6.32e-30 PDB 1R0I "Cadmium-Substituted Rubredoxin" 100.00 54 100.00 100.00 6.32e-30 PDB 1R0J "Nickel-Substituted Rubredoxin" 100.00 54 100.00 100.00 6.32e-30 PDB 1SMM "Crystal Structure Of Cp Rd L41a Mutant In Oxidized State" 100.00 54 98.15 98.15 3.22e-29 PDB 1SMU "Crystal Structure Of Cp Rd L41a Mutant In Reduced State 1 (Drop-Reduced)" 100.00 54 98.15 98.15 3.22e-29 PDB 1SMW "Crystal Structure Of Cp Rd L41a Mutant In Reduced State 2 (Soaked)" 100.00 54 98.15 98.15 3.22e-29 PDB 1T9O "Crystal Structure Of V44g Cp Rubredoxin" 100.00 54 98.15 98.15 8.01e-29 PDB 1T9Q "Crystal Structure Of V44l Cp Rubredoxin" 100.00 54 98.15 100.00 1.27e-29 PDB 4MBS "Crystal Structure Of The Ccr5 Chemokine Receptor" 100.00 414 100.00 100.00 3.30e-35 PDB 4XNV "The Human P2y1 Receptor In Complex With Bptu" 100.00 421 100.00 100.00 4.50e-35 PDB 4XNW "The Human P2y1 Receptor In Complex With Mrs2500" 100.00 421 100.00 100.00 4.50e-35 GB AAA23279 "rubredoxin [Clostridium pasteurianum]" 100.00 54 100.00 100.00 6.32e-30 GB AJA49845 "rubredoxin [Clostridium pasteurianum DSM 525 = ATCC 6013]" 100.00 54 100.00 100.00 6.32e-30 GB AJA53833 "rubredoxin [Clostridium pasteurianum DSM 525 = ATCC 6013]" 100.00 54 100.00 100.00 6.32e-30 GB ELP57804 "Rubredoxin [Clostridium pasteurianum DSM 525 = ATCC 6013]" 100.00 54 100.00 100.00 6.32e-30 GB KER11884 "Rubredoxin domain containing protein [Clostridium pasteurianum DSM 525 = ATCC 6013]" 100.00 54 100.00 100.00 6.32e-30 REF WP_003447684 "rubredoxin [Clostridium pasteurianum]" 100.00 54 100.00 100.00 6.32e-30 SP P00268 "RecName: Full=Rubredoxin; Short=Rd" 100.00 54 100.00 100.00 6.32e-30 stop_ save_ ############# # Ligands # ############# save_FE _Saveframe_category ligand _Mol_type non-polymer _Name_common "FE (FE (III) ION)" _BMRB_code . _PDB_code FE _Molecular_mass 55.845 _Mol_charge 3 _Mol_paramagnetic . _Mol_aromatic no _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Mon Jul 11 10:30:25 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons FE FE FE . 3 . ? 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 $RdxIII 'Clostridium pasteurianum' 1501 Bacteria Monera Clostridium pasteurianum stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_type _Vector_name _Details $RdxIII 'recombinant technology' 'E. coli' Escherichia coli . plasmid . citation_one stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_one _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $RdxIII 5 mM [U-15N] H2O 100 % . stop_ save_ save_sample_two _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $RdxIII 5 mM [U-15N] D2O 100 % . stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_one _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DMX500 _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save__1 _Saveframe_category NMR_applied_experiment _Sample_label . save_ ####################### # Sample conditions # ####################### save_sample_conditions_one _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.0 . n/a temperature 308 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_one _Saveframe_category chemical_shift_reference _Details '15N assignments of Val8, Tyr11, Leu41, Val44' 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 N 15 'methyl protons' ppm . . 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_chemical_shift_one _Saveframe_category assigned_chemical_shifts _Details ; 15N chemical shift assignments for 15N-H Calculated spin density: spin densities are in atomic units VAL 8 0.000954 TYR 11 0.002191 LEU 41 0.001226 VAL 44 0.001007 ; loop_ _Sample_label $sample_one stop_ _Sample_conditions_label $sample_conditions_one _Chem_shift_reference_set_label $chemical_shift_reference_one _Mol_system_component_name RdxIII _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 VAL N N 508.99 . 1 2 . 11 TYR N N 606.0 . 1 3 . 41 LEU N N 521.9 . 1 4 . 44 VAL N N 336.6 . 1 stop_ save_ save_assigned_chemical_shift_two _Saveframe_category assigned_chemical_shifts _Details ; 15N chemical shift assignments for 15N-D Calculated spin density:spin densities are in atomic units VAL 8 0.000923 TYR 11 0.002116 LEU 41 0.001188 VAL 44 0.000972 ; loop_ _Sample_label $sample_two stop_ _Sample_conditions_label $sample_conditions_one _Chem_shift_reference_set_label $chemical_shift_reference_one _Mol_system_component_name RdxIII _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 VAL N N 494.5 . 1 2 . 11 TYR N N 588.3 . 1 3 . 41 LEU N N 507.5 . 1 4 . 44 VAL N N 228.4 . 1 stop_ save_