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- PDB-4cej: Crystal structure of AddAB-DNA-ADPNP complex at 3 Angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 4cej
TitleCrystal structure of AddAB-DNA-ADPNP complex at 3 Angstrom resolution
Components
  • (ATP-DEPENDENT ...) x 2
  • DNA
KeywordsHYDROLASE/DNA / HYDROLASE-DNA COMPLEX / HELICASE-NUCLEASE / DNA BREAKS / DNA REPAIR / SINGLE-STRANDED / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / 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 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 1.3Dec 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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 / _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)298,8798
Polymers297,4663
Non-polymers1,4135
Water1267
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28680 Å2
ΔGint-117.9 kcal/mol
Surface area100480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.437, 152.941, 125.244
Angle α, β, γ (deg.)90.00, 94.30, 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: 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 SUBUNIT B / ATP-DEPENDENT HELICASE/NUCLEASE ADDB


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

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DNA chain , 1 types, 1 molecules X

#3: DNA chain DNA /


Mass: 21477.703 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: ANNEALED HAIRPIN DUPLEX WITH UNPAIRED SINGLE-STRANDED 3' AND 5' TAILS
Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 4 types, 12 molecules

#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsMAGNESIUM ION (MG): COORDINATED BY PROTEIN, ANP AND WATER MOLECULES

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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: 2.8 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1M TRIS-HCL PH 7.5, 11% PEG 4000, 0.1M MAGNESIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96863
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 3→35.55 Å / Num. obs: 57963 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.4
Reflection shellResolution: 3→3.09 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.9 / % possible all: 99.7

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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→29.731 Å / SU ML: 0.37 / σ(F): 1.36 / Phase error: 28.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2434 2923 5 %
Rwork0.2027 --
obs0.2048 57942 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→29.731 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18938 925 72 7 19942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00420458
X-RAY DIFFRACTIONf_angle_d0.77427784
X-RAY DIFFRACTIONf_dihedral_angle_d19.0617848
X-RAY DIFFRACTIONf_chiral_restr0.0323023
X-RAY DIFFRACTIONf_plane_restr0.0043426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.04910.36381240.31122613X-RAY DIFFRACTION100
3.0491-3.10170.35171650.27862608X-RAY DIFFRACTION99
3.1017-3.1580.28891160.26662607X-RAY DIFFRACTION100
3.158-3.21870.35181410.25622619X-RAY DIFFRACTION99
3.2187-3.28430.27631400.24622575X-RAY DIFFRACTION100
3.2843-3.35560.27961320.24612656X-RAY DIFFRACTION100
3.3556-3.43360.31421500.23782565X-RAY DIFFRACTION100
3.4336-3.51930.27621530.22262611X-RAY DIFFRACTION99
3.5193-3.61430.28221260.20722605X-RAY DIFFRACTION100
3.6143-3.72050.25011470.20352651X-RAY DIFFRACTION100
3.7205-3.84030.29271280.20592604X-RAY DIFFRACTION100
3.8403-3.97720.22961600.20352570X-RAY DIFFRACTION100
3.9772-4.13610.2171400.19592632X-RAY DIFFRACTION100
4.1361-4.32380.23571300.1862643X-RAY DIFFRACTION100
4.3238-4.5510.20571160.17792633X-RAY DIFFRACTION100
4.551-4.8350.22791380.17872634X-RAY DIFFRACTION100
4.835-5.20650.2251460.17742632X-RAY DIFFRACTION100
5.2065-5.72710.24131440.19962619X-RAY DIFFRACTION100
5.7271-6.54810.2641520.21062629X-RAY DIFFRACTION100
6.5481-8.22090.22691370.19862645X-RAY DIFFRACTION100
8.2209-29.73270.17171380.17562668X-RAY DIFFRACTION99

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