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- PDB-3k70: Crystal structure of the complete initiation complex of RecBCD -

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Basic information

Entry
Database: PDB / ID: 3k70
TitleCrystal structure of the complete initiation complex of RecBCD
Components
  • DNA (46-MER)
  • Exodeoxyribonuclease V alpha chain
  • Exodeoxyribonuclease V beta chain
  • Exodeoxyribonuclease V gamma chain
KeywordsHYDROLASE/DNA / RECOMBINATION / HELICASE / NUCLEASE / HYDROLASE / DNA REPAIR / ATP-binding / DNA damage / Endonuclease / Exonuclease / Nucleotide-binding / HYDROLASE-DNA COMPLEX
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 / DNA 3'-5' helicase / recombinational repair / 3'-5' DNA helicase activity ...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 / DNA 3'-5' helicase / recombinational repair / 3'-5' DNA helicase activity / 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
RecBCD complex, subunit RecD, N-terminal domain / Arc Repressor Mutant, subunit A - #990 / Recbcd, chain B, domain 2 / Recbcd, chain B, domain 2 / Rossmann fold - #10930 / Arc Repressor Mutant, subunit A - #160 / Lambda Exonuclease; Chain A - #10 / PCRA; domain 4 / PCRA; domain 4 / RecBCD enzyme subunit RecB ...RecBCD complex, subunit RecD, N-terminal domain / Arc Repressor Mutant, subunit A - #990 / Recbcd, chain B, domain 2 / Recbcd, chain B, domain 2 / Rossmann fold - #10930 / Arc Repressor Mutant, subunit A - #160 / Lambda Exonuclease; Chain A - #10 / 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 / PD-(D/E)XK endonuclease-like domain, AddAB-type / PD-(D/E)XK nuclease superfamily / DExx box DNA helicase domain superfamily / AAA 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-like helicase C-terminal domain / UvrD/REP helicase N-terminal domain / PD-(D/E)XK endonuclease-like domain superfamily / UvrD-like helicase, ATP-binding domain / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP type / 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 K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.59 Å
AuthorsSaikrishnan, K. / Wigley, D.B.
Citation
Journal: Embo J. / Year: 2008
Title: DNA binding to RecD: role of the 1B domain in SF1B helicase activity.
Authors: Saikrishnan, K. / Griffiths, S.P. / Cook, N. / Court, R. / Wigley, D.B.
#1: Journal: 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
DepositionOct 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
X: DNA (46-MER)
Y: DNA (46-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)693,48810
Polymers693,4088
Non-polymers802
Water00
1
B: Exodeoxyribonuclease V beta chain
C: Exodeoxyribonuclease V gamma chain
D: Exodeoxyribonuclease V alpha chain
X: DNA (46-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)346,7445
Polymers346,7044
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23840 Å2
ΔGint-87.3 kcal/mol
Surface area123950 Å2
MethodPISA
2
E: Exodeoxyribonuclease V beta chain
F: Exodeoxyribonuclease V gamma chain
G: Exodeoxyribonuclease V alpha chain
Y: DNA (46-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)346,7445
Polymers346,7044
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24090 Å2
ΔGint-91.3 kcal/mol
Surface area124200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.800, 192.900, 334.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe quaternary state of the biomolecule is heterotetrameric: the heterotrimeric protein complexes i.e. chain B,C,D and E,F,G, are bound to DNA chain X and Y, respectively.

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Components

#1: Protein Exodeoxyribonuclease V beta chain / Exodeoxyribonuclease V 135 kDa polypeptide


Mass: 134110.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: b2820, JW2788, recB, rorA / Production host: Escherichia coli (E. coli) / References: UniProt: P08394, exodeoxyribonuclease V
#2: Protein Exodeoxyribonuclease V gamma chain / Exodeoxyribonuclease V 125 kDa polypeptide


Mass: 128974.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: b2822, JW2790, recC / Production host: Escherichia coli (E. coli) / References: UniProt: P07648, exodeoxyribonuclease V
#3: Protein Exodeoxyribonuclease V alpha chain / Exodeoxyribonuclease V 67 kDa polypeptide


Mass: 66990.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: b2819, JW2787, recD / Production host: Escherichia coli (E. coli) / References: UniProt: P04993, exodeoxyribonuclease V
#4: DNA chain DNA (46-MER)


Mass: 16628.859 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthesized DNA
#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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.62 %
Crystal growTemperature: 285 K / pH: 7
Details: 100 mM Hepes pH 7.0, 300 mM Calcium acetate, 6-8% PEG 20000, VAPOR DIFFUSION, HANGING DROP, temperature 285.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1Hepes11
2Calcium acetate11
3PEG 2000011
4Hepes12
5Calcium acetate12
6PEG 2000012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9794
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3.59→50 Å / Num. obs: 97332 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 6.6
Reflection shellResolution: 3.59→3.79 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.351 / % possible all: 97.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W36

1w36


Resolution: 3.59→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflection
Rfree0.296 4709 -
Rwork0.248 --
obs0.248 97231 96.5 %
all-97231 -
Refinement stepCycle: LAST / Resolution: 3.59→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms45060 1870 2 0 46932
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.5
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
LS refinement shellResolution: 3.59→3.83 Å
RfactorNum. reflection% reflection
Rfree0.344 773 -
Rwork0.313 --
obs--97.1 %

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