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

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Basic information

Entry
Database: PDB / ID: 2dwl
TitleCrystal structure of the PriA protein complexed with oligonucleotides
Components
  • 5'-D(*AP*(DC))-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 / DNA 3'-5' helicase / 3'-5' DNA helicase activity / 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 / DNA 3'-5' helicase / 3'-5' DNA helicase activity / replication fork processing / DNA replication initiation / response to gamma radiation / helicase activity / DNA-templated DNA replication / double-strand break repair / DNA recombination / DNA replication / response to antibiotic / ATP hydrolysis activity / 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 / Replication restart protein PriA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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: Version format compliance
Revision 1.3Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author
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
Revision 1.4Oct 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,2226
Polymers48,2226
Non-polymers00
Water00
1
E: 5'-D(*AP*(DC))-3'
A: Primosomal protein N
B: Primosomal protein N


Theoretical massNumber of molelcules
Total (without water)24,1113
Polymers24,1113
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: 5'-D(*AP*(DC))-3'
C: Primosomal protein N
D: Primosomal protein N


Theoretical massNumber of molelcules
Total (without water)24,1113
Polymers24,1113
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.510, 111.510, 260.460
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: DNA chain 5'-D(*AP*(DC))-3'


Mass: 557.431 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein
Primosomal protein N / DNA helicase / 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 (E. coli) / 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; In phosphorus-containing anhydrides

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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: 3.26 Å3/Da / Density % sol: 62.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.8
Details: 0.1M sodium citrate, 0.2M ammonium sulfate, pH 3.8, 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: Dec 16, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 10536 / % possible obs: 99.3 % / Redundancy: 11.1 % / Biso Wilson estimate: 102.2 Å2 / Rsym value: 0.049 / Net I/σ(I): 14.6
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 4.21 / Num. unique all: 1030 / Rsym value: 0.443 / % possible all: 99.2

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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: 3.2→20 Å / σ(F): 2.7
RfactorNum. reflectionSelection details
Rfree0.3019 685 RANDOM
Rwork0.2474 --
all-9672 -
obs-8987 -
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.41 Å
Luzzati d res low-20 Å
Luzzati sigma a0.66 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3296 77 0 0 3373
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0098
X-RAY DIFFRACTIONc_angle_deg1.6795
X-RAY DIFFRACTIONc_angle_d24.4724
X-RAY DIFFRACTIONc_improper_angle_d1.3845
LS refinement shellResolution: 3.2→3.31 Å
RfactorNum. reflection
Rfree0.4206 63
Rwork0.3347 -
obs-681

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