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Open data
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Basic information
Entry | Database: PDB / ID: 1g71 | ||||||
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Title | CRYSTAL STRUCTURE OF PYROCOCCUS FURIOSUS DNA PRIMASE | ||||||
![]() | DNA PRIMASE | ||||||
![]() | REPLICATION / zinc-knuckle | ||||||
Function / homology | ![]() DNA primase activity / primosome complex / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Augustin, M.A. / Huber, R. / Kaiser, J.T. | ||||||
![]() | ![]() Title: Crystal structure of a DNA-dependent RNA polymerase (DNA primase). Authors: Augustin, M.A. / Huber, R. / Kaiser, J.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 159.7 KB | Display | ![]() |
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PDB format | ![]() | 126.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 40841.027 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63 % | ||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: 0.1M Tris/Cl, 2M Ammoniumsulfate, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8.5 | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→17.31 Å / Num. all: 49651 / Num. obs: 46200 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 34.2 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.3→2.44 Å / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 4.6 / Num. unique all: 6179 / % possible all: 84.1 |
Reflection | *PLUS % possible obs: 93 % |
Reflection shell | *PLUS % possible obs: 74.8 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: bulk_solvent correction cns 1.0 / Bsol: 62.4884 Å2 / ksol: 0.38931 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.8 Å2
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Refine analyze | Luzzati coordinate error obs: 0.26 Å / Luzzati d res low obs: 20 Å / Luzzati sigma a obs: 0.07 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→500 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.32 Å / Total num. of bins used: 50
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 500 Å / σ(F): 0 / % reflection Rfree: 9.4 % / Rfactor obs: 0.2108 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.263 / % reflection Rfree: 12.5 % / Rfactor Rwork: 0.232 |