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- PDB-5guj: Crystal structure of the Bacillus subtilis DnaG RNA Polymerase Do... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5guj | ||||||
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Title | Crystal structure of the Bacillus subtilis DnaG RNA Polymerase Domain, natural degradation of full length DnaG | ||||||
![]() | DNA primase | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | ![]() DNA primase DnaG / primosome complex / DNA primase activity / DNA replication, synthesis of primer / DNA-directed RNA polymerase complex / DNA helicase activity / DNA binding / zinc ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhou, Y. / Liu, Z. / Wang, G. | ||||||
![]() | ![]() Title: Structural Insight into the Specific DNA Template Binding to DnaG primase in Bacteria Authors: Zhou, Y. / Luo, H. / Liu, Z. / Yang, M. / Pang, X. / Sun, F. / Wang, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80 KB | Display | ![]() |
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PDB format | ![]() | 57.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425 KB | Display | ![]() |
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Full document | ![]() | 428.2 KB | Display | |
Data in XML | ![]() | 13.9 KB | Display | |
Data in CIF | ![]() | 18.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4e2kS ![]() 5gum S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36987.234 Da / Num. of mol.: 1 / Fragment: UNP residues 112-435 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: dnaG, dnaE, BSU25210 / Plasmid: pGEX-6p-1 / Production host: ![]() ![]() References: UniProt: P05096, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 52.96 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M Sodium citrate tribasic dehydrate, 0.1M Tris hydrochloride (pH 8.5) and 30% (w/v) polyethylene glycol 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 5, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97916 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→29.278 Å / Num. obs: 13480 / % possible obs: 100 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 6.5 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4e2k Resolution: 2.5→29.278 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→29.278 Å
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Refine LS restraints |
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LS refinement shell |
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