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- PDB-4ceh: Crystal structure of AddAB with a forked DNA substrate -

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Basic information

Entry
Database: PDB / ID: 4ceh
TitleCrystal structure of AddAB with a forked DNA substrate
Components
  • ATP-DEPENDENT HELICASE/DEOXYRIBONUCLEASE SUBUNIT B
  • ATP-DEPENDENT HELICASE/NUCLEASE SUBUNIT A
  • DNA
KeywordsHYDROLASE/DNA / HYDROLASE-DNA COMPLEX / HELICASE-NUCLEASE / BACTERIAL PROTEINS / BINDING SITES / DNA BREAKS / DOUBLE-STRANDED / DNA HELICASES / DNA REPAIR / DNA- BINDING PROTEINS / EXODEOXYRIBONUCLEASE V / EXODEOXYRIBONUCLEASES / HOMOLOGOUS RECOMBINATION
Function / homology
Function and homology information


DNA helicase complex / DNA 3'-5' helicase / 5'-3' exonuclease activity / recombinational repair / 3'-5' DNA helicase activity / isomerase activity / 3'-5' exonuclease activity / DNA helicase activity / double-strand break repair via homologous recombination / 4 iron, 4 sulfur cluster binding ...DNA helicase complex / DNA 3'-5' helicase / 5'-3' exonuclease activity / recombinational repair / 3'-5' DNA helicase activity / isomerase activity / 3'-5' exonuclease activity / DNA helicase 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
IRON/SULFUR CLUSTER / DNA / DNA (> 10) / ATP-dependent helicase/deoxyribonuclease subunit B / ATP-dependent helicase/nuclease subunit A
Similarity search - Component
Biological speciesBACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.24 Å
AuthorsKrajewski, W.W. / Wilkinson, M. / Fu, X. / Cronin, N.B. / Wigley, D.
CitationJournal: Nature / Year: 2014
Title: Structural Basis for Translocation by Addab Helicase-Nuclease and its Arrest at Chi Sites.
Authors: Krajewski, W.W. / Fu, X. / Wilkinson, M. / Cronin, N.B. / Dillingham, M.S. / Wigley, D.B.
History
DepositionNov 11, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2Apr 23, 2014Group: Database references
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: exptl_crystal_grow / pdbx_seq_map_depositor_info / struct_biol
Item: _exptl_crystal_grow.temp / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
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 / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)296,2974
Polymers295,9453
Non-polymers3521
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23000 Å2
ΔGint-76.6 kcal/mol
Surface area101310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.373, 96.766, 109.693
Angle α, β, γ (deg.)104.38, 96.11, 90.03
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ATP-DEPENDENT HELICASE/NUCLEASE SUBUNIT A / ATP-DEPENDENT HELICASE/NUCLEASE ADDA / ATP-DEPENDENT HELICASE-NUCLEASE SUBUNIT A


Mass: 141218.844 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria)
Plasmid: PCOLADUET-1 / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834 (DE3)
References: UniProt: P23478, Hydrolases; Acting on ester bonds, DNA helicase
#2: Protein ATP-DEPENDENT HELICASE/DEOXYRIBONUCLEASE SUBUNIT B / ATP-DEPENDENT HELICASE/NUCLEASE ADDB / ATP-DEPENDENT HELICASE-NUCLEASE SUBUNIT B


Mass: 134769.406 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria)
Plasmid: PCOLADUET-1 / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834 (DE3)
References: UniProt: P23477, Hydrolases; Acting on ester bonds, DNA helicase
#3: DNA chain DNA /


Mass: 19956.744 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC CONSTRUCT / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4

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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: 2.99 Å3/Da / Density % sol: 59 % / Description: NONE
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M TRIS-HCL PH 7.5, 15% PEG 4000, 0.8M SODIUM FORMATE, VAPOR DIFFUSION, HANGING DROP, 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.24→39.52 Å / Num. obs: 47940 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.2
Reflection shellResolution: 3.24→3.35 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.3 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHENIXPHASER-MRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3U44

3u44


Resolution: 3.24→29.939 Å / SU ML: 0.42 / σ(F): 1.97 / Phase error: 32.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2638 2374 5 %
Rwork0.2292 --
obs0.231 47592 97.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.24→29.939 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18669 756 8 0 19433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00319901
X-RAY DIFFRACTIONf_angle_d0.61626994
X-RAY DIFFRACTIONf_dihedral_angle_d15.7447625
X-RAY DIFFRACTIONf_chiral_restr0.0242949
X-RAY DIFFRACTIONf_plane_restr0.0033355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.24-3.30610.3751300.2922426X-RAY DIFFRACTION90
3.3061-3.37790.34041300.29252596X-RAY DIFFRACTION95
3.3779-3.45640.32911340.27872673X-RAY DIFFRACTION98
3.4564-3.54270.35281430.26832673X-RAY DIFFRACTION98
3.5427-3.63830.28481360.26092680X-RAY DIFFRACTION98
3.6383-3.74520.29591450.25882652X-RAY DIFFRACTION98
3.7452-3.86580.31871550.25482697X-RAY DIFFRACTION98
3.8658-4.00370.29131400.25962631X-RAY DIFFRACTION99
4.0037-4.16360.30641370.25232669X-RAY DIFFRACTION98
4.1636-4.35250.26911370.24012681X-RAY DIFFRACTION99
4.3525-4.58120.29741250.22772722X-RAY DIFFRACTION99
4.5812-4.86710.25721360.22432688X-RAY DIFFRACTION99
4.8671-5.24110.22681380.21682668X-RAY DIFFRACTION99
5.2411-5.76510.27561580.23482694X-RAY DIFFRACTION99
5.7651-6.59160.25691470.23822684X-RAY DIFFRACTION99
6.5916-8.27550.25151370.20792708X-RAY DIFFRACTION99
8.2755-29.94030.19471460.18192676X-RAY DIFFRACTION99

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