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- PDB-3u4q: Structure of AddAB-DNA complex at 2.8 angstroms -

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Basic information

Entry
Database: PDB / ID: 3u4q
TitleStructure of AddAB-DNA complex at 2.8 angstroms
Components
  • (ATP-dependent ...) x 2
  • DNA (27-MER)
KeywordsHYDROLASE/DNA / Helicase / nuclease / Double strand DNA repair / Protein-DNA complex / HYDROLASE-DNA complex
Function / homology
Function and homology information


DNA helicase complex / 5'-3' exonuclease activity / DNA 3'-5' helicase / recombinational repair / 3'-5' DNA helicase activity / DNA helicase activity / isomerase activity / 3'-5' exonuclease activity / double-strand break repair via homologous recombination / 4 iron, 4 sulfur cluster binding ...DNA helicase complex / 5'-3' exonuclease activity / DNA 3'-5' helicase / recombinational repair / 3'-5' DNA helicase activity / DNA helicase activity / isomerase activity / 3'-5' exonuclease activity / double-strand break repair via homologous recombination / 4 iron, 4 sulfur cluster binding / double-stranded DNA binding / DNA recombination / Hydrolases; Acting on ester bonds / ATP hydrolysis activity / ATP binding / metal ion binding / cytosol
Similarity search - Function
Enzyme I; Chain A, domain 2 - #50 / Helix Hairpins - #1030 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2380 / DNA helicase subunit AddB / DNA helicase subunit AddA / : / ADDB, N-terminal / Lambda Exonuclease; Chain A - #10 / PCRA; domain 4 / PCRA; domain 4 ...Enzyme I; Chain A, domain 2 - #50 / Helix Hairpins - #1030 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2380 / DNA helicase subunit AddB / DNA helicase subunit AddA / : / ADDB, N-terminal / Lambda Exonuclease; Chain A - #10 / PCRA; domain 4 / PCRA; domain 4 / Lambda Exonuclease; Chain A / PD-(D/E)XK endonuclease-like domain, AddAB-type / PD-(D/E)XK nuclease superfamily / UvrD-like DNA helicase C-terminal domain profile. / UvrD-like DNA helicase, C-terminal / UvrD-like helicase C-terminal domain / UvrD/REP helicase N-terminal domain / UvrD-like helicase, ATP-binding domain / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP type / PD-(D/E)XK endonuclease-like domain superfamily / Enzyme I; Chain A, domain 2 / Restriction endonuclease type II-like / Helix Hairpins / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / ATP-dependent helicase/deoxyribonuclease subunit B / ATP-dependent helicase/nuclease subunit A
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSaikrishnan, K. / Krajewski, W. / Wigley, D.
CitationJournal: Embo J. / Year: 2012
Title: Insights into Chi recognition from the structure of an AddAB-type helicase-nuclease complex.
Authors: Saikrishnan, K. / Yeeles, J.T. / Gilhooly, N.S. / Krajewski, W.W. / Dillingham, M.S. / Wigley, D.B.
History
DepositionOct 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent helicase/nuclease subunit A
B: ATP-dependent helicase/deoxyribonuclease subunit B
X: DNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)290,8635
Polymers290,7053
Non-polymers1582
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21580 Å2
ΔGint-95 kcal/mol
Surface area99790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.555, 139.714, 103.093
Angle α, β, γ (deg.)90.00, 105.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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ATP-dependent ... , 2 types, 2 molecules AB

#1: Protein ATP-dependent helicase/nuclease subunit A / ATP-dependent helicase/nuclease AddA


Mass: 141218.844 Da / Num. of mol.: 1 / Mutation: D1172A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: addA, BSU10630 / Production host: Escherichia coli (E. coli)
References: UniProt: P23478, Hydrolases; Acting on ester bonds, DNA helicase
#2: Protein ATP-dependent helicase/deoxyribonuclease subunit B / ATP-dependent helicase/nuclease AddB


Mass: 134769.406 Da / Num. of mol.: 1 / Mutation: D961A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: addB, BSU10620 / Production host: Escherichia coli (E. coli)
References: UniProt: P23477, Hydrolases; Acting on ester bonds, DNA helicase

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DNA chain , 1 types, 1 molecules X

#3: DNA chain DNA (27-MER)


Mass: 14716.432 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 191 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.73 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% polyethylene glycol 4000, 0.1M Tris pH 7.5, 0.8 M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 4, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→99.5 Å / Num. all: 67577 / Num. obs: 64678 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.8→2.95 Å / % possible all: 95.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: dev_750)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→29.918 Å / SU ML: 1.05 / σ(F): 1.36 / Phase error: 29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2865 3203 4.97 %Random
Rwork0.2332 ---
obs0.2358 64447 95.53 %-
all-67462 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.167 Å2 / ksol: 0.343 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.3615 Å2-0 Å2-6.2021 Å2
2---5.0632 Å2-0 Å2
3----2.2984 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18305 555 9 189 19058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00219293
X-RAY DIFFRACTIONf_angle_d0.65526124
X-RAY DIFFRACTIONf_dihedral_angle_d14.6127369
X-RAY DIFFRACTIONf_chiral_restr0.0472854
X-RAY DIFFRACTIONf_plane_restr0.0023277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.90.35033220.31266038X-RAY DIFFRACTION95
2.9-3.0160.34283290.29586171X-RAY DIFFRACTION96
3.016-3.15310.34943110.28796149X-RAY DIFFRACTION96
3.1531-3.31920.31873260.26556178X-RAY DIFFRACTION96
3.3192-3.52680.31733520.24836093X-RAY DIFFRACTION96
3.5268-3.79870.29333270.23176148X-RAY DIFFRACTION96
3.7987-4.180.2843210.22356166X-RAY DIFFRACTION96
4.18-4.78270.24383170.19636171X-RAY DIFFRACTION96
4.7827-6.01770.26993180.22626102X-RAY DIFFRACTION95
6.0177-29.91990.25332800.21256028X-RAY DIFFRACTION92

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