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- PDB-5j1p: Lassa virus L protein cap-snatching endonuclease. Bound to two ma... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5j1p | ||||||
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Title | Lassa virus L protein cap-snatching endonuclease. Bound to two manganese ions | ||||||
![]() | RNA-directed RNA polymerase L | ||||||
![]() | TRANSFERASE / cap-snatching nuclease Lassa transcription | ||||||
Function / homology | ![]() negative stranded viral RNA replication / cap snatching / virion component / host cell cytoplasm / Hydrolases; Acting on ester bonds / hydrolase activity / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Reguera, J. / Cusack, S. | ||||||
![]() | ![]() Title: Comparative Structural and Functional Analysis of Bunyavirus and Arenavirus Cap-Snatching Endonucleases. Authors: Reguera, J. / Gerlach, P. / Rosenthal, M. / Gaudon, S. / Coscia, F. / Gunther, S. / Cusack, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83.8 KB | Display | ![]() |
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PDB format | ![]() | 62 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423.7 KB | Display | ![]() |
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Full document | ![]() | 424.7 KB | Display | |
Data in XML | ![]() | 8.4 KB | Display | |
Data in CIF | ![]() | 10.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5izeC ![]() 5izhC ![]() 5j1nSC C: citing same article ( 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: 20081.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.17 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2mM MnCl, 5mM DPBA, 5 mM MgCl chloride hexahydrate, 0.05 M HEPES-Na pH7 25 % (v/v) PEG MME 550 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Sep 20, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.36→48.43 Å / Num. obs: 8543 / % possible obs: 99.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 22 |
Reflection shell | Resolution: 2.36→2.46 Å / Rmerge(I) obs: 1.208 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5J1N Resolution: 2.36→48.43 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.9 / SU B: 27.472 / SU ML: 0.263 / Cross valid method: THROUGHOUT / ESU R Free: 0.284 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.561 Å2
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Refinement step | Cycle: 1 / Resolution: 2.36→48.43 Å
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Refine LS restraints |
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