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- PDB-5of3: Crystal structure of the heterotrimeric PriSLX primase from S. so... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5of3 | ||||||
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Title | Crystal structure of the heterotrimeric PriSLX primase from S. solfataricus. | ||||||
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![]() | REPLICATION / Primase / DNA-dependent RNA polymerase / DNA replication | ||||||
Function / homology | ![]() primosome complex / DNA primase activity / DNA replication, synthesis of primer / DNA-directed RNA polymerase complex / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / 4 iron, 4 sulfur cluster binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pellegrini, L. / Holzer, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Primer synthesis by a eukaryotic-like archaeal primase is independent of its Fe-S cluster. Authors: Holzer, S. / Yan, J. / Kilkenny, M.L. / Bell, S.D. / Pellegrini, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 300.4 KB | Display | ![]() |
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PDB format | ![]() | 240.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.5 MB | Display | ![]() |
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Full document | ![]() | 2.6 MB | Display | |
Data in XML | ![]() | 49.1 KB | Display | |
Data in CIF | ![]() | 65.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ofnC ![]() 1zt2S S: Starting model for refinement C: citing same article ( |
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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
-Protein , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 37643.895 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: priS, priA, SSO1048 / Production host: ![]() ![]() References: UniProt: Q97Z83, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases #2: Protein | Mass: 35788.969 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: priL, priB, SSO0557, C21_042 / Production host: ![]() ![]() #3: Protein | Mass: 18056.729 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: PriL Source: (gene. exp.) ![]() ![]() Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: SSO0502 / Production host: ![]() ![]() |
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-Non-polymers , 3 types, 10 molecules ![](data/chem/img/APC.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/ZN.gif)
#4: Chemical | ChemComp-APC / #5: Chemical | ChemComp-MN / #6: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.84 Å3/Da / Density % sol: 67.98 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 11% PEG 8000, 21.5% ethylene glycol, 0.1 M bicine/Trizma base pH 8.5, 0.03 M di-, tri-, tetra- and penta-ethyleneglycol (Morpheus crystallization screen, Molecular Dimensions). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 7, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.906→46.91 Å / Num. obs: 54380 / % possible obs: 99.96 % / Redundancy: 9.3 % / Biso Wilson estimate: 89.45 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.03641 / Rsym value: 0.1112 / Net I/σ(I): 15.09 |
Reflection shell | Resolution: 2.906→3.01 Å / Redundancy: 9 % / Rmerge(I) obs: 1.404 / Mean I/σ(I) obs: 1.47 / Num. unique obs: 5392 / CC1/2: 0.527 / Rpim(I) all: 0.4952 / Rsym value: 1.489 / % possible all: 99.93 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1ZT2 Resolution: 2.906→46.91 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 0.05 / Phase error: 29.07
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.906→46.91 Å
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Refine LS restraints |
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LS refinement shell |
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