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Open data
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Basic information
Entry | Database: PDB / ID: 6d7n | |||||||||
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Title | Crystal structure of the W357R/W399R Importin alpha mutant | |||||||||
![]() | Peroxidase,Importin subunit alpha-1 | |||||||||
![]() | TRANSPORT PROTEIN / IMPORTIN / NLS / BIPARTITE / PROTEIN BINDING | |||||||||
Function / homology | ![]() Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / lactoperoxidase activity / peroxidase / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus ...Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / lactoperoxidase activity / peroxidase / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / hydrogen peroxide catabolic process / cytoplasmic stress granule / protein import into nucleus / host cell / DNA-binding transcription factor binding / response to oxidative stress / postsynaptic density / glutamatergic synapse / heme binding / extracellular region / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Pedersen, L.C. / London, R.E. / Gabel, S.A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Variations in nuclear localization strategies among pol X family enzymes. Authors: Kirby, T.W. / Pedersen, L.C. / Gabel, S.A. / Gassman, N.R. / London, R.E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 170.1 KB | Display | ![]() |
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PDB format | ![]() | 132.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5w4eC ![]() 5w4fC ![]() 6d7mC ![]() 5e6qS 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
#1: Protein | Mass: 55272.535 Da / Num. of mol.: 1 / Mutation: W357R, W399R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: PviPRX9, Kpna2, Rch1 / Production host: ![]() ![]() References: UniProt: A0A1S4NYF8, UniProt: P52293, peroxidase | ||
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#2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 62.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.0M triammonium citrate, 0.1M Bis-Tris-Propane |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 28, 2018 / Details: VariMaxHF |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.514 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 32563 / % possible obs: 99.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.064 / Rrim(I) all: 0.164 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1571 / CC1/2: 0.749 / Rpim(I) all: 0.395 / Rrim(I) all: 0.979 / Rsym value: 0.89 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5E6Q Resolution: 2.3→29.287 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 22.77
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→29.287 Å
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Refine LS restraints |
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LS refinement shell |
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