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- PDB-2dwn: Crystal structure of the PriA protein complexed with oligonucleotides -

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Basic information

Entry
Database: PDB / ID: 2dwn
TitleCrystal structure of the PriA protein complexed with oligonucleotides
Components
  • DNA (5'-D(*A*G)-3')
  • Primosomal protein N'
KeywordsHYDROLASE/DNA / PROTEIN-DNA COMPLEX / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


DnaB-DnaC-DnaT-PriA-PriC complex / DnaB-DnaC-DnaT-PriA-PriB complex / plasmid maintenance / primosome complex / DNA replication, synthesis of primer / 3'-5' DNA helicase activity / DNA 3'-5' helicase / replication fork processing / DNA replication initiation / response to gamma radiation ...DnaB-DnaC-DnaT-PriA-PriC complex / DnaB-DnaC-DnaT-PriA-PriB complex / plasmid maintenance / primosome complex / DNA replication, synthesis of primer / 3'-5' DNA helicase activity / DNA 3'-5' helicase / replication fork processing / DNA replication initiation / response to gamma radiation / helicase activity / DNA-templated DNA replication / double-strand break repair / DNA recombination / DNA replication / hydrolase activity / response to antibiotic / DNA binding / zinc ion binding / ATP binding
Similarity search - Function
PriA, 3(prime) DNA-binding domain / Primosomal protein N' / PriA DNA helicase, Cys-rich region (CRR) domain / Primosomal protein N', 3' DNA-binding domain / Primosomal protein N, C-terminal domain / Primosomal protein N', 3' DNA-binding domain superfamily / : / : / 3'DNA-binding domain (3'BD) / Primosomal protein N C-terminal domain ...PriA, 3(prime) DNA-binding domain / Primosomal protein N' / PriA DNA helicase, Cys-rich region (CRR) domain / Primosomal protein N', 3' DNA-binding domain / Primosomal protein N, C-terminal domain / Primosomal protein N', 3' DNA-binding domain superfamily / : / : / 3'DNA-binding domain (3'BD) / Primosomal protein N C-terminal domain / PriA DNA helicase Cys-rich region (CRR) domain / Primosomal protein N'-like, winged helix / GIY-YIG endonuclease / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / ATP-dependent DNA helicase PriA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsSasaki, K. / Ose, T. / Tanaka, T. / Masai, H. / Maenaka, K. / Kohda, D.
CitationJournal: EMBO J. / Year: 2007
Title: Structural basis of the 3'-end recognition of a leading strand in stalled replication forks by PriA.
Authors: Sasaki, K. / Ose, T. / Okamoto, N. / Maenaka, K. / Tanaka, T. / Masai, H. / Saito, M. / Shirai, T. / Kohda, D.
History
DepositionAug 15, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 27, 2019Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / struct_ref / struct_ref_seq
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type
Revision 2.0Mar 13, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_poly / entity_poly_seq / pdbx_poly_seq_scheme / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.auth_comp_id / _atom_site.group_PDB ..._atom_site.auth_comp_id / _atom_site.group_PDB / _atom_site.label_comp_id / _chem_comp.id / _chem_comp.mon_nstd_flag / _entity.pdbx_description / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id
Revision 2.1Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Primosomal protein N'
B: Primosomal protein N'
C: Primosomal protein N'
D: Primosomal protein N'
E: DNA (5'-D(*A*G)-3')
F: DNA (5'-D(*A*G)-3')


Theoretical massNumber of molelcules
Total (without water)48,3026
Polymers48,3026
Non-polymers00
Water00
1
A: Primosomal protein N'
B: Primosomal protein N'
E: DNA (5'-D(*A*G)-3')


Theoretical massNumber of molelcules
Total (without water)24,1513
Polymers24,1513
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-21 kcal/mol
Surface area12480 Å2
MethodPISA, PQS
2
C: Primosomal protein N'
D: Primosomal protein N'
F: DNA (5'-D(*A*G)-3')


Theoretical massNumber of molelcules
Total (without water)24,1513
Polymers24,1513
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-24 kcal/mol
Surface area12200 Å2
MethodPISA, PQS
3
A: Primosomal protein N'
B: Primosomal protein N'
E: DNA (5'-D(*A*G)-3')

A: Primosomal protein N'
B: Primosomal protein N'
E: DNA (5'-D(*A*G)-3')


Theoretical massNumber of molelcules
Total (without water)48,3026
Polymers48,3026
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_545y+2/3,x-2/3,-z+1/31
Buried area12640 Å2
ΔGint-72 kcal/mol
Surface area21470 Å2
MethodPISA
4
C: Primosomal protein N'
D: Primosomal protein N'
F: DNA (5'-D(*A*G)-3')

C: Primosomal protein N'
D: Primosomal protein N'
F: DNA (5'-D(*A*G)-3')


Theoretical massNumber of molelcules
Total (without water)48,3026
Polymers48,3026
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z1
Buried area13290 Å2
ΔGint-75 kcal/mol
Surface area20810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.250, 112.250, 260.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein
Primosomal protein N' / ATP-dependent helicase PriA / Replication factor Y


Mass: 11776.790 Da / Num. of mol.: 4 / Fragment: Residues 1-105
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: priA, b3935, JW3906 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P17888, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: DNA chain DNA (5'-D(*A*G)-3')


Mass: 597.455 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)

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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: 3.3 Å3/Da / Density % sol: 62.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.6
Details: 0.1M sodium citrate, 0.4M ammonium sulfate, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium citrate11
2ammonium sulfate11
3sodium citrate12
4ammonium sulfate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 5, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.35→50 Å / Num. obs: 9392 / % possible obs: 99.9 % / Redundancy: 11 % / Biso Wilson estimate: 113.2 Å2 / Rsym value: 0.052 / Net I/σ(I): 15.4
Reflection shellResolution: 3.35→3.47 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 2.73 / Num. unique all: 931 / Rsym value: 0.387 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2D7E

2d7e


Resolution: 3.35→20 Å / σ(F): 2.7
RfactorNum. reflectionSelection details
Rfree0.3332 646 RANDOM
Rwork0.2807 --
all-8798 -
obs-8152 -
Refine analyze
FreeObs
Luzzati coordinate error0.62 Å0.46 Å
Luzzati d res low-20 Å
Luzzati sigma a0.75 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 3.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3296 38 0 0 3334
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0106
X-RAY DIFFRACTIONc_angle_deg1.6928
X-RAY DIFFRACTIONc_angle_d23.8474
X-RAY DIFFRACTIONc_improper_angle_d1.3655
LS refinement shellResolution: 3.35→3.47 Å
RfactorNum. reflection
Rfree0.3937 63
Rwork0.337 -
obs-670

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