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Yorodumi- PDB-5guj: Crystal structure of the Bacillus subtilis DnaG RNA Polymerase Do... -
+Open data
-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 | ||||||
Components | DNA primasePrimase | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information 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 | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Zhou, Y. / Liu, Z. / Wang, G. | ||||||
Citation | Journal: Sci Rep / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5guj.cif.gz | 80 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5guj.ent.gz | 57.9 KB | Display | PDB format |
PDBx/mmJSON format | 5guj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/5guj ftp://data.pdbj.org/pub/pdb/validation_reports/gu/5guj | HTTPS FTP |
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-Related structure data
Related structure data | 4e2kS 5gum S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: dnaG, dnaE, BSU25210 / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) References: UniProt: P05096, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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