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- PDB-4lil: Crystal structure of the catalytic subunit of human primase bound... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4lil | ||||||
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Title | Crystal structure of the catalytic subunit of human primase bound to UTP and Mn | ||||||
![]() | DNA primase small subunit![]() | ||||||
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Function / homology | ![]() DNA primase AEP / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vaithiyalingam, S. / Eichman, B.F. / Chazin, W.J. | ||||||
![]() | ![]() Title: Insights into Eukaryotic Primer Synthesis from Structures of the p48 Subunit of Human DNA Primase. Authors: Vaithiyalingam, S. / Arnett, D.R. / Aggarwal, A. / Eichman, B.F. / Fanning, E. / Chazin, W.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 166.9 KB | Display | ![]() |
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PDB format | ![]() | 139.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 559 KB | Display | ![]() |
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Full document | ![]() | 563.3 KB | Display | |
Data in XML | ![]() | 16.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 46471.223 Da / Num. of mol.: 1 Fragment: Catalytic subunit p48, UNP residues 1-390 (delta 360-379) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P49642, ![]() | ||||
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#2: Chemical | ChemComp-ZN / | ||||
#3: Chemical | #4: Chemical | ChemComp-UTP / | ![]() #5: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.15 % |
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Crystal grow![]() | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2M K/Na Tartrate and 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 16, 2012 |
Radiation | Monochromator: 0.99 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.6→50 Å / Num. all: 15266 / Num. obs: 15266 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.2 % / Rsym value: 0.76 / Net I/σ(I): 37.6 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 14.6 % / Mean I/σ(I) obs: 6.1 / Rsym value: 0.454 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→44.731 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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