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Yorodumi- PDB-7asi: Fixed-target serial femtosecond crystallography using in cellulo ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7asi | ||||||||||||
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Title | Fixed-target serial femtosecond crystallography using in cellulo grown Neurospora crassa HEX-1 microcrystals. (Chips 1+2) | ||||||||||||
Components | eIF-5a domain-containing protein | ||||||||||||
Keywords | STRUCTURAL PROTEIN / in cellulo crystals / Woronin body / septal pore sealing | ||||||||||||
Function / homology | Function and homology information positive regulation of translational termination / positive regulation of translational elongation / translation elongation factor activity / ribosome binding / RNA binding Similarity search - Function | ||||||||||||
Biological species | Neurospora crassa (fungus) | ||||||||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.704 Å | ||||||||||||
Model details | Chip 1+2 | ||||||||||||
Authors | Lahey-Rudolph, J.M. / Schoenherr, R. / Barthelmess, M. / Fischer, P. / Seuring, C. / Wagner, A. / Meents, A. / Redecke, L. | ||||||||||||
Funding support | Germany, 3items
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Citation | Journal: Iucrj / Year: 2021 Title: Fixed-target serial femtosecond crystallography using in cellulo grown microcrystals. Authors: Lahey-Rudolph, J.M. / Schonherr, R. / Barthelmess, M. / Fischer, P. / Seuring, C. / Wagner, A. / Meents, A. / Redecke, L. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7asi.cif.gz | 68.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7asi.ent.gz | 50.3 KB | Display | PDB format |
PDBx/mmJSON format | 7asi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/as/7asi ftp://data.pdbj.org/pub/pdb/validation_reports/as/7asi | HTTPS FTP |
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-Related structure data
Related structure data | 7asxC 1khiS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 19221.742 Da / Num. of mol.: 1 / Mutation: Met1_Tyr2insGly; Ser175_*insAla Source method: isolated from a genetically manipulated source Details: Recombinant baculovirus production in Escherichia coli DH10EmBacY (Geneva Biotech, BacToBac system). Lipofection with Escort IV reagent. P3 recombinant baculovirus stock used for infection ...Details: Recombinant baculovirus production in Escherichia coli DH10EmBacY (Geneva Biotech, BacToBac system). Lipofection with Escort IV reagent. P3 recombinant baculovirus stock used for infection of insect cells at MOI 1. Source: (gene. exp.) Neurospora crassa (fungus) / Gene: GE21DRAFT_1527 Plasmid: modified pFastBac1 vector containing the sequence 5 -ATGGGCGCCTAA-3 between the BamHI and HindIII restriction sites Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A0B0EDT5 |
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#2: Water | ChemComp-HOH / |
Compound details | The in cellulo crystallized Neurospora crassa HEX-1 forms a polymeric helical spiral with 12 ...The in cellulo crystallized Neurospora crassa HEX-1 forms a polymeric helical spiral with 12 monomers per full turn, or 6 homodimeric units per full turn. The homodimeric assembly features an identical interaction on opposite faces that propagates the spiral. This results in the six-fold symmetry of the crystals that is consistently observed in native Woronin bodies |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.93 % |
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Crystal grow | Temperature: 300.15 K / Method: in cell Details: Neurospora crassa HEX-1 P3 rBV-infected Sf9 cells at multiplicity of infection 1, cultivated in serum-free ESF921 medium |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.312 Å |
Detector | Type: CS-PAD CXI-1 / Detector: PIXEL / Date: Oct 2, 2017 / Details: Beryllium lenses |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.312 Å / Relative weight: 1 |
Reflection | Resolution: 1.704→39.9 Å / Num. obs: 22635 / % possible obs: 99.99 % / Redundancy: 124.12 % / Biso Wilson estimate: 18.31 Å2 / CC1/2: 0.964 / CC star: 0.991 / R split: 0.162 / Net I/σ(I): 5.421 |
Reflection shell | Resolution: 1.704→1.744 Å / Redundancy: 16.4 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1469 / CC1/2: 0.16 / CC star: 0.525 / R split: 0.189 / % possible all: 99.86 |
Serial crystallography measurement | Collection time total: 0.25 hours / Focal spot size: 1 µm2 / Pulse duration: 27.5 fsec. / Pulse photon energy: 9.45 keV / Source distance: 0.116 m / XFEL pulse repetition rate: 120 Hz |
Serial crystallography sample delivery | Description: fixed target / Method: fixed target |
Serial crystallography sample delivery fixed target | Description: micro-patterned single-crystalline silicon microchips Details: scanning speed matched to 120 Hz pulse repetition rate Motion control: attachment to Roadrunner II / Sample dehydration prevention: humidor, helium chamber / Sample solvent: ESF921 insect cell medium / Sample unit size: 12 µm / Support base: Chips glued to aluminium support frame / Velocity horizontal: 2.5 / Velocity vertical: 100 |
Serial crystallography data reduction | Crystal hits: 19676 / Frames failed index: 6286 / Frames indexed: 13390 / Frames total: 87450 / Lattices indexed: 15224 / XFEL pulse events: 87450 / XFEL run numbers: 6,9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1khi Resolution: 1.704→29.365 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.95 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.52 Å2 / Biso mean: 25.3897 Å2 / Biso min: 3.79 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.704→29.365 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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