5LD2 Hydrolase date Jun 23, 2016
title Cryo-Em Structure Of Recbcd+Dna Complex Revealing Activated Domain
authors M.Wilkinson, Y.Chaban, D.B.Wigley
compound source
Molecule: Recbcd Enzyme Subunit Recb,Recbcd Enzyme Subunit 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, Exodeoxyribonuclease V 135 Kda Polypeptide,Exodeoxyribonucl Beta Chain,Exonuclease V Subunit Recb,Exov Subunit Recb, Helicasenuclease Recbcd Subunit Recb,Exodeoxyribonuclease Polypeptide,Exodeoxyribonuclease V Beta Chain,Exonuclease V Recb,Exov Subunit Recb,Helicasenuclease Recbcd Subunit Rec
Ec: 3.1.11.5,3.1.11.5,3.1.11.5
Engineered: Yes
Mutation: Yes
Other_details: Residues 913-932 Modelled As Poly-Alanine In Reflect Uncertainty Of The Exact Position Of This Loop Due Density.;
 Organism_scientific: Escherichia Coli (Strain K12)
Organism_taxid: 83333
Strain: K12
Gene: Recb, Ior, Rora, B2820, Jw2788
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Petduet

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 (Strain K12)
Organism_taxid: 83333
Strain: K12
Gene: Recc, B2822, Jw2790
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Prsfduet

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 (Strain K12)
Organism_taxid: 83333
Strain: K12
Gene: Recd, Hope, B2819, Jw2787
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcdfduet

Molecule: Fork-Hairpin Dna (70-Mer)
Chain: X
Engineered: Yes
Other_details: Hairpin=38-42 Duplex=13-37&43-67 5'Tail=1-12 3'Tail=68-70
Synthetic: Yes
Organism_scientific: Endothia Gyrosa
Organism_taxid: 40263
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 3.83 Å
ligand ANP, MG enzyme Hydrolase E.C.3.1.11.5 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
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 referenceMechanism for nuclease regulation in RecBCD., Wilkinson M, Chaban Y, Wigley DB, Elife. 2016 Sep 20;5. pii: e18227. doi: 10.7554/eLife.18227. PMID:27644322
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (490 Kb) [Save to disk]
  • Biological Unit Coordinates (5ld2.pdb1.gz) 484 Kb
  • LPC: Ligand-Protein Contacts for 5LD2
  • CSU: Contacts of Structural Units for 5LD2
  • Retrieve 5LD2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5LD2 from S2C, [Save to disk]
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  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
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    • Visual 3D analysis of 5LD2
  • 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: [5ld2_B] [5ld2_C] [5ld2_D] [5ld2] [5ld2_X]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5LD2: [AAA ] by SMART
    • Other resources with information on 5LD2
  • Community annotation for 5LD2 at PDBWiki (http://pdbwiki.org)

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