+Open data
-Basic information
Entry | Database: PDB / ID: 4zc0 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of a dodecameric bacterial helicase | ||||||
Components | Replicative DNA helicase | ||||||
Keywords | HYDROLASE / Helicase ATPase DNA replication / dodecamer | ||||||
Function / homology | Function and homology information primosome complex / DNA replication, synthesis of primer / DNA unwinding involved in DNA replication / DNA helicase activity / DNA helicase / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 6.7 Å | ||||||
Authors | Bazin, A. / Cherrier, M.V. / Gutsche, I. / Timmins, J. / Terradot, L. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2015 Title: Structure and primase-mediated activation of a bacterial dodecameric replicative helicase. Authors: Bazin, A. / Cherrier, M.V. / Gutsche, I. / Timmins, J. / Terradot, L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4zc0.cif.gz | 223.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4zc0.ent.gz | 181.5 KB | Display | PDB format |
PDBx/mmJSON format | 4zc0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/4zc0 ftp://data.pdbj.org/pub/pdb/validation_reports/zc/4zc0 | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 59590.605 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: dnaB, HP_1362 / Production host: Escherichia coli (E. coli) / References: UniProt: O25916, DNA helicase #2: Chemical | ChemComp-TBR / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.98 Å3/Da / Density % sol: 69.11 % / Description: Cubic |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Polyethylene glycol 3350 26%, 100 mM Tris pH 8.6 and 200 mM Lithium Sulphate PH range: 8 |
-Data collection
Diffraction | Mean temperature: 173 K | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1.2546 Å | |||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 18, 2013 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 6.7→48.61 Å / Num. obs: 6960 / % possible obs: 99.7 % / Redundancy: 44.3 % / Rmerge(I) obs: 0.177 / Rsym value: 0.177 / Net I/σ(I): 18.3 | |||||||||
Reflection shell | Resolution: 6.7→7.06 Å / Redundancy: 45.6 % / Rmerge(I) obs: 4.725 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 6.7→47.245 Å / SU ML: 1.08 / Cross valid method: FREE R-VALUE / σ(F): 0.07 / Phase error: 34.42 / 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: 6.7→47.245 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|