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- PDB-1kac: KNOB DOMAIN FROM ADENOVIRUS SEROTYPE 12 IN COMPLEX WITH DOMAIN 1 ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kac | ||||||
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Title | KNOB DOMAIN FROM ADENOVIRUS SEROTYPE 12 IN COMPLEX WITH DOMAIN 1 OF ITS CELLULAR RECEPTOR CAR | ||||||
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Function / homology | ![]() AV node cell-bundle of His cell adhesion involved in cell communication / cell adhesive protein binding involved in AV node cell-bundle of His cell communication / AV node cell to bundle of His cell communication / homotypic cell-cell adhesion / epithelial structure maintenance / regulation of AV node cell action potential / gamma-delta T cell activation / apicolateral plasma membrane / germ cell migration / transepithelial transport ...AV node cell-bundle of His cell adhesion involved in cell communication / cell adhesive protein binding involved in AV node cell-bundle of His cell communication / AV node cell to bundle of His cell communication / homotypic cell-cell adhesion / epithelial structure maintenance / regulation of AV node cell action potential / gamma-delta T cell activation / apicolateral plasma membrane / germ cell migration / transepithelial transport / cardiac muscle fiber development / cell-cell junction organization / negative regulation of cardiac muscle cell proliferation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Bewley, M.C. / Springer, K. / Zhang, Y.B. / Freimuth, P. / Flanagan, J.M. | ||||||
![]() | ![]() Title: Structural analysis of the mechanism of adenovirus binding to its human cellular receptor, CAR. Authors: Bewley, M.C. / Springer, K. / Zhang, Y.B. / Freimuth, P. / Flanagan, J.M. | ||||||
Validation Report | ![]() ![]() ![]() | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmcif format | ![]() ![]() ![]() |
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PDB format | ![]() ![]() |
PDBML Plus | ![]() |
Others | ![]() |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell | γ α β
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Components
#1: Protein | Mass: 19944.477 Da / Num. of mol.: 1 / Fragment: KNOB Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 13640.500 Da / Num. of mol.: 1 / Fragment: DOMAIN 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.6 Å3/Da / Density % sol: 78 % | ||||||||||||||||||
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Crystal grow![]() | pH: 6.2 / Details: 900MM AMMONIUM SULPHATE ON 100MM MES, PH 6.2 | ||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 99 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.6→40 Å / Num. obs: 24636 / % possible obs: 100 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.7 |
Reflection shell | Resolution: 2.6→2.7 Å / Rmerge(I) obs: 0.35 / % possible all: 100 |
Reflection shell | *PLUS % possible obs: 100 % / Mean I/σ(I) obs: 6 |
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Processing
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Refinement | Method to determine structure![]()
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Solvent computation | Bsol: 61 Å2 / ksol: 0.43 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 2.9 % / Rfactor obs: 0.22 / Rfactor Rfree![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 44.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.7 |