data_444 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of the DNA binding wing of the gene-V encoded single-stranded DNA binding protein of the filamentous bacteriophage M13 ; _BMRB_accession_number 444 _BMRB_flat_file_name bmr444.str _Entry_type update _Submission_date 1995-07-31 _Accession_date 1996-04-13 _Entry_origination BMRB _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 'van Duynhoven' John P.M. . 2 Folkers P. J.M. . 3 Stassen A. P.M. . 4 Harmsen B. J.M. . 5 Konings R. N.H. . 6 Hilbers C. W. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 98 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-06-11 revision BMRB 'Complete natural source information' 1999-06-14 revision BMRB 'Converted to BMRB NMR-STAR V 2.1 format' 1996-04-13 revision BMRB 'Link to the Protein Data Bank added' 1996-03-25 reformat BMRB 'Converted to the BMRB 1996-03-01 STAR flat-file format' 1995-07-31 original BMRB 'Last release in original BMRB flat-file format' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full ; van Duynhoven, John P.M., Folkers, P.J.M., Stassen, A.P.M., Harmsen, B.J.M., Konings, R.N.H., Hilbers, C. W., "Structure of the DNA binding wing of the gene-V encoded single-stranded DNA binding protein of the filamentous bacteriophage M13," FEBS Lett. 261, 1-4 (1990). ; _Citation_title ; Structure of the DNA binding wing of the gene-V encoded single-stranded DNA binding protein of the filamentous bacteriophage M13 ; _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 'van Duynhoven' John P.M. . 2 Folkers P. J.M. . 3 Stassen A. P.M. . 4 Harmsen B. J.M. . 5 Konings R. N.H. . 6 Hilbers C. W. . stop_ _Journal_abbreviation 'FEBS Lett.' _Journal_volume 261 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1 _Page_last 4 _Year 1990 _Details . save_ ################################## # Molecular system description # ################################## save_system_gene_V_protein _Saveframe_category molecular_system _Mol_system_name 'gene V protein' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'gene V protein' $gene_V_protein stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic ? _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_gene_V_protein _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'gene V protein' _Name_variant Y41H _Molecular_mass . _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 87 _Mol_residue_sequence ; MIKVEIKPSQAQFTTRSGVS RQGKPYSLNEQLCYVDLGNE HPVLVKITLDEGQPAYAPGL YTVHLSSFKVGQFGSLMIDR LRLVPAK ; loop_ _Residue_seq_code _Residue_label 1 MET 2 ILE 3 LYS 4 VAL 5 GLU 6 ILE 7 LYS 8 PRO 9 SER 10 GLN 11 ALA 12 GLN 13 PHE 14 THR 15 THR 16 ARG 17 SER 18 GLY 19 VAL 20 SER 21 ARG 22 GLN 23 GLY 24 LYS 25 PRO 26 TYR 27 SER 28 LEU 29 ASN 30 GLU 31 GLN 32 LEU 33 CYS 34 TYR 35 VAL 36 ASP 37 LEU 38 GLY 39 ASN 40 GLU 41 HIS 42 PRO 43 VAL 44 LEU 45 VAL 46 LYS 47 ILE 48 THR 49 LEU 50 ASP 51 GLU 52 GLY 53 GLN 54 PRO 55 ALA 56 TYR 57 ALA 58 PRO 59 GLY 60 LEU 61 TYR 62 THR 63 VAL 64 HIS 65 LEU 66 SER 67 SER 68 PHE 69 LYS 70 VAL 71 GLY 72 GLN 73 PHE 74 GLY 75 SER 76 LEU 77 MET 78 ILE 79 ASP 80 ARG 81 LEU 82 ARG 83 LEU 84 VAL 85 PRO 86 ALA 87 LYS 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 2039 "gene V protein" 100.00 87 100.00 100.00 2.62e-56 PDB 1AE2 "Mutant L32r Of Gene V Protein (Single-Stranded Dna Binding Protein)" 100.00 87 97.70 98.85 2.02e-54 PDB 1AE3 "Mutant R82c Of Gene V Protein (Single-Stranded Dna Binding Protein)" 98.85 86 97.67 98.84 3.13e-53 PDB 1GKH "Mutant K69h Of Gene V Protein (Single-Stranded Dna Binding Protein)" 100.00 87 97.70 98.85 2.11e-54 PDB 1GVP "Gene V Protein (Single-Stranded Dna Binding Protein)" 100.00 87 98.85 100.00 2.42e-55 PDB 1VQB "Gene V Protein (Single-Stranded Dna Binding Protein)" 100.00 87 98.85 100.00 2.42e-55 PDB 1VQG "Gene V Protein Mutant With Ile 47 Replaced By Leu 47 (I47l)" 100.00 87 97.70 100.00 6.52e-55 PDB 1VQH "Gene V Protein Mutant With Ile 47 Replaced By Met 47 (I47m)" 100.00 87 97.70 100.00 6.96e-55 PDB 1VQI "Gene V Protein Mutant With Ile 47 Replaced By Val 47 (I47v)" 100.00 87 97.70 100.00 4.04e-55 PDB 1VQJ "Gene V Protein Mutant With Val 35 Replaced By Ile 35 (V35i)" 100.00 87 97.70 100.00 3.86e-55 PDB 1YHA "Crystal Structures Of Y41h And Y41f Mutants Of Gene V Protein From Ff Phage Suggest Possible Protein-Protein Interactions In Gv" 100.00 87 100.00 100.00 2.62e-56 PDB 1YHB "Crystal Structures Of Y41h And Y41f Mutants Of Gene V Protein From Ff Phage Suggest Possible Protein-Protein Interactions In Gv" 100.00 87 98.85 98.85 5.97e-55 PDB 2GN5 "Refined Structure Of The Gene 5 Dna Binding Protein From Bacteriophage Fd" 100.00 87 98.85 100.00 2.42e-55 PDB 2GVA "Refined Solution Structure Of The Tyr 41--> His Mutant Of The M13 Gene V Protein. A Comparison With The Crystal Structure" 100.00 87 100.00 100.00 2.62e-56 PDB 2GVB "Refined Solution Structure Of The Tyr 41--> His Mutant Of The M13 Gene V Protein. A Comparison With The Crystal Structure" 100.00 87 100.00 100.00 2.62e-56 DBJ BAF74204 "protein V [Enterobacteria phage f1]" 100.00 87 98.85 100.00 2.42e-55 DBJ BAF74214 "protein V [Enterobacteria phage f1]" 100.00 87 98.85 100.00 2.42e-55 EMBL CAA23858 "helix destabilising protein [Enterobacteria phage M13]" 100.00 87 98.85 100.00 2.42e-55 EMBL CAA23868 "unnamed protein product [Enterobacteria phage f1]" 100.00 87 98.85 100.00 2.42e-55 GB AAA32211 "protein V [Enterobacteria phage f1]" 100.00 87 98.85 100.00 2.42e-55 GB AAA32226 "gene V protein, partial [Enterobacteria phage f1]" 51.72 45 97.78 100.00 4.12e-23 GB AAA32305 "V [Enterobacteria phage fd]" 100.00 87 98.85 100.00 2.42e-55 GB AAF75603 "cytosolic single-stranded DNA binding protein pV [Filamentous phage cloning vector fd-tet]" 100.00 87 98.85 100.00 2.42e-55 GB AAM73885 "cytosolic single-stranded DNA binding protein pV [Filamentous phage display vector f8-5]" 100.00 87 98.85 100.00 2.42e-55 PRF 0812197G DNA,phage 100.00 87 98.85 100.00 2.42e-55 REF NP_510887 "helix destabilising protein [Enterobacteria phage M13]" 100.00 87 98.85 100.00 2.42e-55 REF YP_009111289 "protein V [Enterobacteria phage f1]" 100.00 87 98.85 100.00 2.42e-55 REF YP_009111299 "V [Enterobacteria phage fd]" 100.00 87 98.85 100.00 2.42e-55 SP P69542 "RecName: Full=DNA-Binding protein G5P; Short=G5P; AltName: Full=GPV; AltName: Full=Single-stranded DNA-binding protein" 100.00 87 98.85 100.00 2.42e-55 SP P69543 "RecName: Full=DNA-Binding protein G5P; Short=G5P; AltName: Full=GPV; AltName: Full=Single-stranded DNA-binding protein" 100.00 87 98.85 100.00 2.42e-55 SP P69544 "RecName: Full=DNA-Binding protein G5P; Short=G5P; AltName: Full=Single-stranded DNA-binding protein" 100.00 87 98.85 100.00 2.42e-55 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Strain $gene_V_protein 'M13 filamentous phage' 12420 Virus . Filamentous phage 'gp-V Y41H' 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 $gene_V_protein 'not available' . Escherichia coli K37 . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_one _Saveframe_category sample _Sample_type solution _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_list _Saveframe_category NMR_spectrometer _Manufacturer unknown _Model unknown _Field_strength 0 _Details 'spectrometer information not available' save_ ############################# # NMR applied experiments # ############################# save__1 _Saveframe_category NMR_applied_experiment _Sample_label $sample_one save_ ####################### # Sample conditions # ####################### save_sample_condition_set_one _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 5.2 . na temperature 298 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_shift_reference_par_set_one _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_citation_label _Correction_value_citation_label TSP H . . ppm 0 . . . . . $entry_citation $entry_citation 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_assignment_data_set_one _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_one stop_ _Sample_conditions_label $sample_condition_set_one _Chem_shift_reference_set_label $chem_shift_reference_par_set_one _Mol_system_component_name 'gene V 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 . 13 PHE H H 7.83 . 1 2 . 13 PHE HA H 5.4 . 1 3 . 13 PHE HB2 H 3.68 . 2 4 . 13 PHE HB3 H 3.26 . 2 5 . 13 PHE HD1 H 6.93 . 1 6 . 13 PHE HD2 H 6.93 . 1 7 . 13 PHE HE1 H 7.27 . 1 8 . 13 PHE HE2 H 7.27 . 1 9 . 13 PHE HZ H 7.27 . 1 10 . 14 THR H H 9.21 . 1 11 . 14 THR HA H 4.73 . 1 12 . 14 THR HB H 4.23 . 1 13 . 14 THR HG2 H 1.28 . 1 14 . 15 THR H H 8.87 . 1 15 . 15 THR HA H 5.35 . 1 16 . 15 THR HB H 3.92 . 1 17 . 15 THR HG2 H 1.23 . 1 18 . 16 ARG H H 9.36 . 1 19 . 16 ARG HA H 4.75 . 1 20 . 16 ARG HB2 H 1.88 . 2 21 . 16 ARG HB3 H 1.8 . 2 22 . 16 ARG HG2 H 1.6 . 1 23 . 16 ARG HG3 H 1.6 . 1 24 . 17 SER H H 8.56 . 1 25 . 17 SER HA H 5.01 . 1 26 . 17 SER HB2 H 3.81 . 1 27 . 17 SER HB3 H 3.81 . 1 28 . 18 GLY H H 7.66 . 1 29 . 18 GLY HA2 H 4.07 . 2 30 . 18 GLY HA3 H 3.54 . 2 31 . 19 VAL H H 8.41 . 1 32 . 19 VAL HA H 4.57 . 1 33 . 19 VAL HB H 1.89 . 1 34 . 19 VAL HG1 H .88 . 1 35 . 19 VAL HG2 H .88 . 1 36 . 20 SER H H 9.15 . 1 37 . 20 SER HA H 4.7 . 1 38 . 20 SER HB2 H 4.38 . 2 39 . 20 SER HB3 H 4.08 . 2 40 . 21 ARG H H 9.13 . 1 41 . 21 ARG HA H 4.26 . 1 42 . 21 ARG HB2 H 1.93 . 1 43 . 21 ARG HB3 H 1.93 . 1 44 . 21 ARG HG2 H 1.76 . 1 45 . 21 ARG HG3 H 1.76 . 1 46 . 21 ARG HD2 H 3.26 . 1 47 . 21 ARG HD3 H 3.26 . 1 48 . 22 GLN H H 7.93 . 1 49 . 22 GLN HA H 4.42 . 1 50 . 22 GLN HB2 H 2.34 . 2 51 . 22 GLN HB3 H 1.93 . 2 52 . 22 GLN HG2 H 2.5 . 2 53 . 22 GLN HG3 H 2.39 . 2 54 . 23 GLY H H 8.19 . 1 55 . 23 GLY HA2 H 4.2 . 2 56 . 23 GLY HA3 H 3.64 . 2 57 . 24 LYS H H 7.67 . 1 58 . 24 LYS HA H 4.92 . 1 59 . 24 LYS HB2 H 1.93 . 2 60 . 24 LYS HB3 H 1.77 . 2 61 . 25 PRO HA H 5.04 . 1 62 . 25 PRO HB2 H 2.34 . 2 63 . 25 PRO HB3 H 1.95 . 2 64 . 25 PRO HG2 H 2.15 . 2 65 . 25 PRO HG3 H 2.04 . 2 66 . 25 PRO HD2 H 4.09 . 2 67 . 25 PRO HD3 H 3.78 . 2 68 . 26 TYR H H 8.37 . 1 69 . 26 TYR HA H 4.94 . 1 70 . 26 TYR HB2 H 2.98 . 1 71 . 26 TYR HB3 H 2.98 . 1 72 . 26 TYR HD1 H 6.89 . 1 73 . 26 TYR HD2 H 6.89 . 1 74 . 26 TYR HE1 H 6.48 . 1 75 . 26 TYR HE2 H 6.48 . 1 76 . 27 SER H H 8.39 . 1 77 . 27 SER HA H 4.97 . 1 78 . 27 SER HB2 H 3.69 . 2 79 . 27 SER HB3 H 3.63 . 2 80 . 28 LEU H H 8.94 . 1 81 . 28 LEU HA H 4.65 . 1 82 . 28 LEU HB2 H 1.6 . 1 83 . 28 LEU HB3 H 1.6 . 1 84 . 28 LEU HG H 1.6 . 1 85 . 28 LEU HD1 H .9 . 2 86 . 28 LEU HD2 H .85 . 2 87 . 29 ASN H H 9.06 . 1 88 . 29 ASN HA H 5.47 . 1 89 . 29 ASN HB2 H 2.48 . 2 90 . 29 ASN HB3 H 1.62 . 2 91 . 30 GLU H H 8.93 . 1 92 . 30 GLU HA H 5.54 . 1 93 . 30 GLU HB2 H 1.99 . 1 94 . 30 GLU HB3 H 1.99 . 1 95 . 31 GLN H H 9.31 . 1 96 . 31 GLN HA H 4.9 . 1 97 . 31 GLN HB2 H 2.03 . 1 98 . 31 GLN HB3 H 2.03 . 1 stop_ save_