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Yorodumi- PDB-2dwl: Crystal structure of the PriA protein complexed with oligonucleotides -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dwl | ||||||
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Title | Crystal structure of the PriA protein complexed with oligonucleotides | ||||||
Components |
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Keywords | HYDROLASE/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 / replication fork processing / DNA unwinding involved in DNA replication / 3'-5' DNA helicase activity / 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 / replication fork processing / DNA unwinding involved in DNA replication / 3'-5' DNA helicase activity / 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 | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Sasaki, K. / Ose, T. / Tanaka, T. / Masai, H. / Maenaka, K. / 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dwl.cif.gz | 86.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dwl.ent.gz | 67.2 KB | Display | PDB format |
PDBx/mmJSON format | 2dwl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dwl_validation.pdf.gz | 457.7 KB | Display | wwPDB validaton report |
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Full document | 2dwl_full_validation.pdf.gz | 484.3 KB | Display | |
Data in XML | 2dwl_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | 2dwl_validation.cif.gz | 26.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dw/2dwl ftp://data.pdbj.org/pub/pdb/validation_reports/dw/2dwl | HTTPS FTP |
-Related structure data
Related structure data | 2d7eSC 2d7gC 2d7hC 2dwmC 2dwnC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 557.431 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Protein | 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
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 62.29 % | ||||||||||||||||||||
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Crystal grow | Temperature: 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 |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 16, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2D7E Resolution: 3.2→20 Å / σ(F): 2.7
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.31 Å
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