5MBV Dna Binding Protein date Nov 08, 2016
title Cryo-Em Structure Of Lambda Phage Protein Gams Bound To Recb
authors M.Wilkinson, Y.Chaban, D.B.Wigley
compound source
Molecule: Recbcd Enzyme Subunit Recb
Chain: B
Synonym: Exodeoxyribonuclease V 135 Kda Polypeptide, Exodeoxyribonuclease V Beta Chain,Exonuclease V Subunit Rec Subunit Recb,Helicasenuclease Recbcd Subunit Recb;
Ec: 3.1.11.5
Engineered: Yes
 Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Recb, Ior, Rora, B2820, Jw2788
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Petduet-1

Molecule: Recbcd Enzyme Subunit Recc
Chain: C
Synonym: Exodeoxyribonuclease V 125 Kda Polypeptide, Exodeoxyribonuclease V Gamma Chain,Exonuclease V Subunit Re Subunit Recc;
Ec: 3.1.11.5
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Recc, B2822, Jw2790
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Prsfduet-1

Molecule: Recbcd Enzyme Subunit Recd
Chain: D
Synonym: Exodeoxyribonuclease V 67 Kda Polypeptide, Exodeoxyribonuclease V Alpha Chain,Exonuclease V Subunit Re Subunit Recd,Helicasenuclease Recbcd Subunit Recd;
Ec: 3.1.11.5
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Recd, Hope, B2819, Jw2787
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcdfduet-1

Molecule: Host-Nuclease Inhibitor Protein Gam
Chain: A, E
Engineered: Yes
Mutation: Yes
Other_details: Gaml Is Cleaved At Position Y44 When Express E.Coli Into Gams (See Paper - Pubmed Id 17544443). We Had T Gene Synthesised To Start At M41 For This Project. It Purif Dimer.
Organism_scientific: Enterobacteria Phage Lambda
Organism_taxid: 10710
Gene: Gam, Gamma
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 3.80 Å
ligand
enzyme Hydrolase E.C.3.1.11.5 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, E


B
  • DNA helicase activity
  • nuclease activity
  • exonuclease activity
  • 3'-5' DNA helicase activity


    • C
  • DNA helicase activity
  • nuclease activity
  • exonuclease activity


    • D
  • DNA helicase activity
  • nuclease activity
  • exonuclease activity
  • single-stranded DNA-dependen...


    • Primary referenceStructural basis for the inhibition of RecBCD by Gam and its synergistic antibacterial effect with quinolones., Wilkinson M, Troman L, Wan Nur Ismah WA, Chaban Y, Avison MB, Dillingham MS, Wigley DB, Elife. 2016 Dec 23;5. pii: e22963. doi: 10.7554/eLife.22963. PMID:28009252
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (494 Kb) [Save to disk]
  • Biological Unit Coordinates (5mbv.pdb1.gz) 489 Kb
  • CSU: Contacts of Structural Units for 5MBV
  • Retrieve 5MBV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5MBV from S2C, [Save to disk]
    • View 5MBV in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 5MBV
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5mbv_A] [5mbv] [5mbv_B] [5mbv_D] [5mbv_E] [5mbv_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5MBV
  • Community annotation for 5MBV at PDBWiki (http://pdbwiki.org)

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