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- PDB-1w36: RecBCD:DNA complex -

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Basic information

Entry
Database: PDB / ID: 1w36
TitleRecBCD:DNA complex
Components
  • DNA HAIRPIN
  • EXODEOXYRIBONUCLEASE V ALPHA CHAIN
  • EXODEOXYRIBONUCLEASE V BETA CHAIN
  • EXODEOXYRIBONUCLEASE V GAMMA CHAIN
KeywordsRECOMBINATION / HELICASE / NUCLEASE / HYDROLASE / DNA REPAIR
Function / homology
Function and homology information


exodeoxyribonuclease V / exodeoxyribonuclease V activity / exodeoxyribonuclease V complex / clearance of foreign intracellular DNA / DNA translocase activity / DNA 5'-3' helicase / single-stranded DNA helicase activity / recombinational repair / 3'-5' DNA helicase activity / DNA 3'-5' helicase ...exodeoxyribonuclease V / exodeoxyribonuclease V activity / exodeoxyribonuclease V complex / clearance of foreign intracellular DNA / DNA translocase activity / DNA 5'-3' helicase / single-stranded DNA helicase activity / recombinational repair / 3'-5' DNA helicase activity / DNA 3'-5' helicase / ATP-dependent activity, acting on DNA / DNA helicase activity / DNA endonuclease activity / isomerase activity / helicase activity / double-strand break repair via homologous recombination / response to radiation / 5'-3' DNA helicase activity / DNA recombination / DNA damage response / magnesium ion binding / ATP hydrolysis activity / DNA binding / ATP binding / cytosol
Similarity search - Function
Arc Repressor Mutant, subunit A - #990 / Recbcd, chain B, domain 2 / Recbcd, chain B, domain 2 / Rossmann fold - #10930 / RecBCD complex, subunit RecD, N-terminal domain / Arc Repressor Mutant, subunit A - #160 / PCRA; domain 4 / PCRA; domain 4 / RecBCD enzyme subunit RecB / RecBCD enzyme subunit RecD ...Arc Repressor Mutant, subunit A - #990 / Recbcd, chain B, domain 2 / Recbcd, chain B, domain 2 / Rossmann fold - #10930 / RecBCD complex, subunit RecD, N-terminal domain / Arc Repressor Mutant, subunit A - #160 / PCRA; domain 4 / PCRA; domain 4 / RecBCD enzyme subunit RecB / RecBCD enzyme subunit RecD / RecBCD enzyme subunit RecC / RecC, C-terminal / RecBCD enzyme subunit RecD, N-terminal domain / : / Exodeoxyribonuclease V, gamma subunit / RecC C-terminal domain / RecBCD enzyme subunit RecD, N-terminal domain / Lambda Exonuclease; Chain A - #10 / PD-(D/E)XK endonuclease-like domain, AddAB-type / PD-(D/E)XK nuclease superfamily / Lambda Exonuclease; Chain A / AAA domain / DExx box DNA helicase domain superfamily / UvrD-like helicase C-terminal domain / UvrD-like DNA helicase C-terminal domain profile. / UvrD-like DNA helicase, C-terminal / UvrD-like helicase C-terminal domain / UvrD-like helicase C-terminal domain / UvrD/REP helicase N-terminal domain / PD-(D/E)XK endonuclease-like domain superfamily / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP type / UvrD-like helicase, ATP-binding domain / AAA domain / Restriction endonuclease type II-like / : / Arc Repressor Mutant, subunit A / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Alpha-Beta Complex / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / RecBCD enzyme subunit RecD / RecBCD enzyme subunit RecC / RecBCD enzyme subunit RecB
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.1 Å
AuthorsSingleton, M.R. / Dillingham, M.S. / Gaudier, M. / C Kowalczykowski, S. / Wigley, D.B.
CitationJournal: Nature / Year: 2004
Title: Crystal Structure of Recbcd Enzyme Reveals a Machine for Processing DNA Breaks
Authors: Singleton, M.R. / Dillingham, M.S. / Gaudier, M. / Kowalczykowski, S.C. / Wigley, D.B.
History
DepositionJul 13, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: EXODEOXYRIBONUCLEASE V BETA CHAIN
C: EXODEOXYRIBONUCLEASE V GAMMA CHAIN
D: EXODEOXYRIBONUCLEASE V ALPHA CHAIN
E: EXODEOXYRIBONUCLEASE V BETA CHAIN
F: EXODEOXYRIBONUCLEASE V GAMMA CHAIN
G: EXODEOXYRIBONUCLEASE V ALPHA CHAIN
Y: DNA HAIRPIN
Z: DNA HAIRPIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)686,57110
Polymers686,4918
Non-polymers802
Water00
1
B: EXODEOXYRIBONUCLEASE V BETA CHAIN
C: EXODEOXYRIBONUCLEASE V GAMMA CHAIN
D: EXODEOXYRIBONUCLEASE V ALPHA CHAIN
Y: DNA HAIRPIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)343,2865
Polymers343,2464
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: EXODEOXYRIBONUCLEASE V BETA CHAIN
F: EXODEOXYRIBONUCLEASE V GAMMA CHAIN
G: EXODEOXYRIBONUCLEASE V ALPHA CHAIN
Z: DNA HAIRPIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)343,2865
Polymers343,2464
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)132.602, 187.234, 335.369
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein EXODEOXYRIBONUCLEASE V BETA CHAIN / RECB


Mass: 134110.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P08394, exodeoxyribonuclease V
#2: Protein EXODEOXYRIBONUCLEASE V GAMMA CHAIN / RECC


Mass: 128974.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P07648, exodeoxyribonuclease V
#3: Protein EXODEOXYRIBONUCLEASE V ALPHA CHAIN / RECD


Mass: 66990.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P04993, exodeoxyribonuclease V
#4: DNA chain DNA HAIRPIN


Mass: 13170.455 Da / Num. of mol.: 2 / Source method: obtained synthetically
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.53 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.1→46.8 Å / Num. obs: 151577 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 3.1→46.84 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 4860428.14 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.296 7373 4.9 %RANDOM
Rwork0.242 ---
obs0.242 151577 99.9 %-
Displacement parametersBiso mean: 68.8 Å2
Refinement stepCycle: LAST / Resolution: 3.1→46.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms44597 1546 2 0 46145
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.16
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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