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- PDB-3uc9: Crystal Structure of Yeast Irc6p - A Novel Type of Conserved Clat... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3uc9 | ||||||
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Title | Crystal Structure of Yeast Irc6p - A Novel Type of Conserved Clathrin Accessory Protein | ||||||
![]() | Increased recombination centers protein 6 | ||||||
![]() | RECOMBINATION / Rossmann-fold / Clathrin accessory factor | ||||||
Function / homology | Rossmann fold - #11960 / Increased recombination centres protein 6 / vesicle-mediated transport / protein-macromolecule adaptor activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Increased recombination centers protein 6![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gorynia, S. / Payne, G.S. / Cascio, D. / Sawaya, M.R. | ||||||
![]() | ![]() Title: Yeast Irc6p is a novel type of conserved clathrin coat accessory factor related to small G proteins. Authors: Gorynia, S. / Lorenz, T.C. / Costaguta, G. / Daboussi, L. / Cascio, D. / Payne, G.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 | ![]() | 88.1 KB | Display | ![]() |
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PDB format | ![]() | 66.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424.6 KB | Display | ![]() |
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Full document | ![]() | 425.9 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 11.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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: 27419.041 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: IRC6, YFR043C / Plasmid: pET-28a / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M ammonium sulfate, 0.1 MES, 30 % w/v PEG monomethyl ether 5000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→80 Å / Num. obs: 18511 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 14.74 Å2 / Rmerge(I) obs: 0.066 / Χ2: 1.006 / Net I/σ(I): 13.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 48.24 Å2 / Biso mean: 25.72 Å2 / Biso min: 4.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→27.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.848 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 32.8344 Å / Origin y: 17.5676 Å / Origin z: -7.1722 Å
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