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Yorodumi- PDB-2d7g: Crystal structure of the aa complex of the N-terminal domain of PriA -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d7g | |||||||||
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Title | Crystal structure of the aa complex of the N-terminal domain of PriA | |||||||||
Components |
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Keywords | HYDROLASE / 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 / DNA unwinding involved in DNA replication / replication fork processing / 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 / DNA unwinding involved in DNA replication / replication fork processing / 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) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | |||||||||
Authors | Sasaki, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d7g.cif.gz | 85.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d7g.ent.gz | 67.2 KB | Display | PDB format |
PDBx/mmJSON format | 2d7g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/2d7g ftp://data.pdbj.org/pub/pdb/validation_reports/d7/2d7g | HTTPS FTP |
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-Related 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: 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 (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 | Mass: 581.456 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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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: 3.35 Å3/Da / Density % sol: 63.27 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Detector: CCD / Date: Oct 29, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→20 Å / Num. obs: 9099 / % possible obs: 93.1 % |
Reflection shell | Resolution: 3.3→3.51 Å / Rmerge(I) obs: 0.335 / Num. unique all: 1306 / % possible all: 89 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→20 Å / Cross valid method: through / σ(F): 2.5 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.51 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
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