[English] 日本語
Yorodumi- PDB-4m4w: Mechanistic implications for the bacterial primosome assembly of ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4m4w | ||||||
---|---|---|---|---|---|---|---|
Title | Mechanistic implications for the bacterial primosome assembly of the structure of a helicase-helicase loader complex | ||||||
Components |
| ||||||
Keywords | REPLICATION / primase / helicase loader / DnaB / DnaG / DnaI / DNA replication | ||||||
Function / homology | Function and homology information DNA primase DnaG / DNA primase activity / DNA 5'-3' helicase / primosome complex / DNA replication, synthesis of primer / DNA unwinding involved in DNA replication / DNA-directed RNA polymerase complex / DNA helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA replication ...DNA primase DnaG / DNA primase activity / DNA 5'-3' helicase / primosome complex / DNA replication, synthesis of primer / DNA unwinding involved in DNA replication / DNA-directed RNA polymerase complex / DNA helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA replication / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / identical protein binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) Bacillus subtilis subsp. subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.1 Å | ||||||
Authors | Liu, B. / Eliason, W.K. / Steitz, T.A. | ||||||
Citation | Journal: Nat Commun / Year: 2013 Title: Structure of a helicase-helicase loader complex reveals insights into the mechanism of bacterial primosome assembly. Authors: Liu, B. / Eliason, W.K. / Steitz, T.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4m4w.cif.gz | 759.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4m4w.ent.gz | 633 KB | Display | PDB format |
PDBx/mmJSON format | 4m4w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4m4w_validation.pdf.gz | 579 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4m4w_full_validation.pdf.gz | 825.2 KB | Display | |
Data in XML | 4m4w_validation.xml.gz | 164.5 KB | Display | |
Data in CIF | 4m4w_validation.cif.gz | 217 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/4m4w ftp://data.pdbj.org/pub/pdb/validation_reports/m4/4m4w | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 50699.445 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: dnaB / Plasmid: pET21d(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9X4C9 #2: Protein | Mass: 16796.490 Da / Num. of mol.: 3 / Fragment: Helicase Binding Domain (UNP residues 455-597) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: dnaG / Plasmid: pET21d(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9X4D0 #3: Protein | Mass: 36991.152 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria) Strain: 168 / Gene: BSU28980, dnaI, ytxA / Plasmid: pET21d(+) / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P06567 |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.79 Å3/Da / Density % sol: 74.29 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion / pH: 8 Details: 11-13% w/v PEG3350, 0.2 M lithium sulfate, 50 mM TRIS, pH 8.0-8.3, VAPOR DIFFUSION, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 11, 2010 / Details: mirrors |
Radiation | Monochromator: Cryo-Cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 6→50 Å / Num. all: 26476 / Num. obs: 26476 / % possible obs: 95.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rsym value: 0.175 / Net I/σ(I): 3.7 |
Reflection shell | Resolution: 6→6.21 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 0.5 / Num. unique all: 2472 / Rsym value: 1 / % possible all: 90.7 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 6.1→20 Å / Cor.coef. Fo:Fc: 0.768 / Cor.coef. Fo:Fc free: 0.73 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 3.614 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 140.281 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 6.1→20 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 6.1→6.242 Å / Total num. of bins used: 20
|