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- PDB-2d7g: Crystal structure of the aa complex of the N-terminal domain of PriA -

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Basic information

Entry
Database: PDB / ID: 2d7g
TitleCrystal structure of the aa complex of the N-terminal domain of PriA
Components
  • DNA (5'-D(P*AP*A)-3')
  • Primosomal protein N'
KeywordsHYDROLASE / PROTEIN-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 / replication fork processing / DNA unwinding involved in DNA replication / DNA replication initiation / helicase activity ...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 / replication fork processing / DNA unwinding involved in DNA replication / DNA replication initiation / helicase activity / response to gamma radiation / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / 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'-like, winged helix / 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'-like, winged helix / 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 / GIY-YIG endonuclease / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / 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 / Primosomal protein N'
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsSasaki, K. / Ose, T. / Maenaka, K. / Masai, H. / Kohda, D.
Citation
Journal: 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.
#1: Journal: Biochim.Biophys.Acta / Year: 2006
Title: Crystallization and preliminary crystallographic analysis of the N-terminal domain of PriA from Escherichia coli
Authors: Sasaki, K. / Ose, T. / Tanaka, T. / Mizukoshi, T. / Ishigaki, T. / Maenaka, K. / Masai, H. / Kohda, D.
History
DepositionNov 21, 2005Deposition 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 2.0Mar 27, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ref / struct_ref_seq
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_ec / _entity.type / _entity_name_com.name / _entity_src_gen.gene_src_genus / _entity_src_gen.gene_src_strain / _entity_src_gen.host_org_genus / _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 2.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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(P*AP*A)-3')
F: DNA (5'-D(P*AP*A)-3')
G: DNA (5'-D(P*AP*A)-3')
H: DNA (5'-D(P*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)49,4338
Polymers49,4338
Non-polymers00
Water0
1
A: Primosomal protein N'
B: Primosomal protein N'
E: DNA (5'-D(P*AP*A)-3')
F: DNA (5'-D(P*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)24,7164
Polymers24,7164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Primosomal protein N'
D: Primosomal protein N'
G: DNA (5'-D(P*AP*A)-3')
H: DNA (5'-D(P*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)24,7164
Polymers24,7164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.820, 110.820, 267.183
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: pET-15b / 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(P*AP*A)-3')


Mass: 581.456 Da / Num. of mol.: 4 / 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: 3.35 Å3/Da / Density % sol: 63.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 12% PEG 6000, 0.1M sodium acetate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorDetector: CCD / Date: Oct 29, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→20 Å / Num. obs: 9099 / % possible obs: 93.1 %
Reflection shellResolution: 3.3→3.51 Å / Rmerge(I) obs: 0.335 / Num. unique all: 1306 / % possible all: 89

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SHARPphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→20 Å / Cross valid method: through / σ(F): 2.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.309 633 -RANDOM
Rwork0.26 ---
obs-9099 93.1 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.04 Å212.71 Å20 Å2
2--7.04 Å20 Å2
3----14.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.6 Å
Refinement stepCycle: LAST / Resolution: 3.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3265 0 84 0 3349
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d1.11
LS refinement shellResolution: 3.3→3.51 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.385 113 8 %
Rwork0.335 1306 -
obs-9099 89 %

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