[English] 日本語
![](img/lk-miru.gif)
- PDB-2dwm: Crystal structure of the PriA protein complexed with oligonucleotides -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2dwm | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the PriA protein complexed with oligonucleotides | ||||||
![]() |
| ||||||
![]() | HYDROLASE/DNA / PROTEIN-DNA COMPLEX / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sasaki, K. / Ose, T. / Tanaka, T. / Masai, H. / Maenaka, K. / Kohda, D. | ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 86.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 67.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 466.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 497.7 KB | Display | |
Data in XML | ![]() | 21.1 KB | Display | |
Data in CIF | ![]() | 27.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2d7eSC ![]() 2d7gC ![]() 2d7hC ![]() 2dwlC ![]() 2dwnC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: DNA chain | Mass: 572.442 Da / Num. of mol.: 3 / 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.) ![]() ![]() ![]() ![]() References: UniProt: P17888, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.25 Å3/Da / Density % sol: 62.21 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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: 3.15→50 Å / Num. obs: 11411 / % possible obs: 99.9 % / Redundancy: 10.8 % / Biso Wilson estimate: 111.4 Å2 / Rsym value: 0.071 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 3.15→3.26 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 4.77 / Num. unique all: 1126 / Rsym value: 0.425 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2D7E Resolution: 3.15→20 Å / σ(F): 2.7
| ||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.15→20 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
LS refinement shell | Resolution: 3.15→3.26 Å
|