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- PDB-8cd6: structure of HEX-1 (cyto V2) from N. crassa grown in living insec... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8cd6 | ||||||||||||
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Title | structure of HEX-1 (cyto V2) from N. crassa grown in living insect cells, diffracted at 100K and resolved using CrystFEL | ||||||||||||
![]() | Woronin body major protein | ||||||||||||
![]() | STRUCTURAL PROTEIN / naturally crystallizing / Woronin body / self-assembly / HEX-1 / in vivo | ||||||||||||
Function / homology | ![]() 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 | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Boger, J. / Schoenherr, R. / Lahey-Rudolph, J.M. / Harms, M. / Kaiser, J. / Nachtschatt, S. / Wobbe, M. / Koenig, P. / Bourenkov, G. / Schneider, T. / Redecke, L. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 51.6 KB | Display | ![]() |
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PDB format | ![]() | 28.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 393.7 KB | Display | ![]() |
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Full document | ![]() | 395.3 KB | Display | |
Data in XML | ![]() | 4.8 KB | Display | |
Data in CIF | ![]() | 6.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8c51C ![]() 8c53C ![]() 8c5kC ![]() 8cd4C ![]() 8cd5C ![]() 8cgxC ![]() 8cgyC ![]() 1khiS C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 19466.979 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.56 % |
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Crystal grow | Temperature: 300 K / Method: in cell Details: baculovirus infected and grown in Trichoplusia ni (High Five) cells in adhesion culture (MOI 1) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 24, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→49.1 Å / Num. obs: 30212 / % possible obs: 99.81 % / Redundancy: 278 % / Biso Wilson estimate: 33.91 Å2 / CC1/2: 0.9953 / Net I/σ(I): 8.15 |
Reflection shell | Resolution: 1.85→1.916 Å / Num. unique obs: 1646 / CC1/2: 0.4226 |
Serial crystallography sample delivery | Method: fixed target |
Serial crystallography sample delivery fixed target | Description: Micro mesh mount |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 1khi Resolution: 1.85→49.1 Å / SU ML: 0.3009 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.9498 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 40.88 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→49.1 Å
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Refine LS restraints |
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LS refinement shell |
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