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Yorodumi- PDB-8c5k: HEX-1 (in cellulo, in situ) crystallized and diffracted in High F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8c5k | |||||||||
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Title | HEX-1 (in cellulo, in situ) crystallized and diffracted in High Five cells. Growth and SX data collection at 296 K on CrystalDirect plates | |||||||||
Components | Woronin body major protein | |||||||||
Keywords | STRUCTURAL PROTEIN / Woronin body / self-assembly / HEX-1 / in vivo | |||||||||
Function / homology | Function and homology information Woronin body / positive regulation of translational termination / positive regulation of translational elongation / cell septum / translational elongation / translation elongation factor activity / ribosome binding / RNA binding Similarity search - Function | |||||||||
Biological species | Neurospora crassa OR74A (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å | |||||||||
Authors | Lahey-Rudolph, J.M. / Schoenherr, R. / Boger, J. / Harms, M. / Kaiser, J. / Nachtschatt, S. / Wobbe, M. / Duden, R. / Koenig, P. / Bourenkov, G. ...Lahey-Rudolph, J.M. / Schoenherr, R. / Boger, J. / Harms, M. / Kaiser, J. / Nachtschatt, S. / Wobbe, M. / Duden, R. / Koenig, P. / Bourenkov, G. / Schneider, T. / Redecke, L. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Nat Commun / Year: 2024 Title: A streamlined approach to structure elucidation using in cellulo crystallized recombinant proteins, InCellCryst. Authors: Schonherr, R. / Boger, J. / Lahey-Rudolph, J.M. / Harms, M. / Kaiser, J. / Nachtschatt, S. / Wobbe, M. / Duden, R. / Konig, P. / Bourenkov, G. / Schneider, T.R. / Redecke, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c5k.cif.gz | 66.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c5k.ent.gz | 48.5 KB | Display | PDB format |
PDBx/mmJSON format | 8c5k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8c5k_validation.pdf.gz | 417.6 KB | Display | wwPDB validaton report |
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Full document | 8c5k_full_validation.pdf.gz | 417.6 KB | Display | |
Data in XML | 8c5k_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | 8c5k_validation.cif.gz | 9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/8c5k ftp://data.pdbj.org/pub/pdb/validation_reports/c5/8c5k | HTTPS FTP |
-Related structure data
Related structure data | 8c51C 8c53C 8cd4C 8cd5C 8cd6C 8cgxC 8cgyC 1khiS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
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: 19150.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neurospora crassa OR74A (fungus) / Strain: ATCC 24698 / Gene: hex-1, NCU08332 / Plasmid: pFB1 / Details (production host): cyto / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P87252 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.59 % / Description: hexagonal, spindle-like shape |
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Crystal grow | Temperature: 300 K / Method: in cell Details: Infected with rBV HEX-1 and grown in High-Five cells in suspension culture, MOI 1 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.971 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.971 Å / Relative weight: 1 |
Reflection | Resolution: 2.16→49.09 Å / Num. obs: 11210 / % possible obs: 99.96 % / Redundancy: 246 % / Biso Wilson estimate: 24.1 Å2 / CC1/2: 0.998 / CC star: 0.999 / R split: 0.0586 / Net I/σ(I): 10.41 |
Reflection shell | Resolution: 2.16→2.237 Å / Redundancy: 68 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1066 / CC1/2: 0.595 / CC star: 0.864 / R split: 0.871 / % possible all: 99.72 |
Serial crystallography sample delivery | Description: CrystalDirect plate (96 well) / Method: fixed target |
Serial crystallography sample delivery fixed target | Description: in cellulo in situ growth Details: 90 degree mounting of Crystal Direct plate on goniometer, well polymer foil coating with D-lys Sample dehydration prevention: crystallization foil seal / Sample holding: CrystalDirect / Sample solvent: ESF921 insect cell medium with 25% FBS / Support base: goniometer |
Serial crystallography data reduction | Crystal hits: 91354 / Frames indexed: 55640 / Frames total: 595419 / Lattices indexed: 57052 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1khi Resolution: 2.16→49.09 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.15 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.16→49.09 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / % reflection obs: 100 %
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