+
Open data
-
Basic information
Entry | Database: PDB / ID: 6dcr | ||||||
---|---|---|---|---|---|---|---|
Title | E. coli PriA helicase winged helix domain deletion protein | ||||||
![]() | Primosomal protein N' | ||||||
![]() | DNA BINDING PROTEIN / PriA / Helicase / DNA replication restart | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Satyshur, K.A. / Windgassen, T.A. / Keck, J.L. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structure-specific DNA replication-fork recognition directs helicase and replication restart activities of the PriA helicase. Authors: Windgassen, T.A. / Leroux, M. / Satyshur, K.A. / Sandler, S.J. / Keck, J.L. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 704.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 592.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 472.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 496.4 KB | Display | |
Data in XML | ![]() | 47.6 KB | Display | |
Data in CIF | ![]() | 68.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6dgdC ![]() 4nl4S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 77282.500 Da / Num. of mol.: 2 / Mutation: delta 114-174 Source method: isolated from a genetically manipulated source Details: deletion of the winged helix domain (114-174) Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: priA, b3935, JW3906 / Plasmid: pET15b-EcoliPriA / Production host: ![]() ![]() References: UniProt: P17888, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.93 % Description: Thin square sheets. Formed within one day and collected/froze after the second day. |
---|---|
Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 50 mM HEPES-HCl pH 7.5, 9.5 % PEG 4000, 4 % Isopropanol, 8 % glycerol, 50 mM sodium malonate, and 25-100 mM sodium fluoride |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12712 Å / Relative weight: 1 |
Reflection | Resolution: 1.978→48.832 Å / Num. obs: 101849 / % possible obs: 96.75 % / Redundancy: 3.7 % / Biso Wilson estimate: 47.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05904 / Rpim(I) all: 0.03598 / Rrim(I) all: 0.06941 / Net I/σ(I): 11.18 |
Reflection shell | Resolution: 1.978→2.049 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.299 / Mean I/σ(I) obs: 1.03 / Num. unique obs: 9857 / CC1/2: 0.374 / Rpim(I) all: 0.7657 / Rrim(I) all: 1.513 / % possible all: 94.98 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4NL4 removing the winged helix domain Resolution: 1.978→48.832 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.67 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.978→48.832 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|