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- PDB-4d1g: Crystal structure of the fiber head domain of the Atadenovirus sn... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4d1g | ||||||
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Title | Crystal structure of the fiber head domain of the Atadenovirus snake adenovirus 1, native, second P212121 crystal form | ||||||
![]() | FIBER PROTEIN | ||||||
![]() | VIRAL PROTEIN | ||||||
Function / homology | Adenovirus fibre protein / Attachment protein shaft domain superfamily / viral capsid / cell adhesion / symbiont entry into host cell / host cell nucleus / virion attachment to host cell / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Fiber protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Singh, A.K. / van Raaij, M.J. | ||||||
![]() | ![]() Title: Crystal structure of the fibre head domain of the Atadenovirus Snake Adenovirus 1. Authors: Singh, A.K. / Menendez-Conejero, R. / San Martin, C. / van Raaij, M.J. #1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. Year: 2013 Title: Crystallization of the C-terminal domain of the fibre protein from snake adenovirus 1, an atadenovirus. Authors: Singh, A.K. / Menendez-Conejero, R. / San Martin, C. / van Raaij, M.J. #2: Journal: Arch.Virol. / Year: 1993 Title: Physicochemical Properties and Cytopathogenicity of an Adenovirus-Like Agent Isolated from Corn Snake (Elaphe Guttata). Authors: Juhasz, A. / Ahne, W. #3: Journal: Virus Res. / Year: 2008 Title: Completion of the Genome Analysis of Snake Adenovirus Type 1, a Representative of the Reptilian Lineage within the Novel Genus Atadenovirus. Authors: Farkas, S.L. / Harrach, B. / Benko, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 282.9 KB | Display | ![]() |
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PDB format | ![]() | 228.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.8 MB | Display | ![]() |
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Full document | ![]() | 2.8 MB | Display | |
Data in XML | ![]() | 57.7 KB | Display | |
Data in CIF | ![]() | 81 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4d0uC ![]() 4d0vSC ![]() 4d1fC ![]() 4umiC ![]() 4d1h C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15370.116 Da / Num. of mol.: 12 / Fragment: FIBER HEAD DOMAIN, RESIDUES 234-339 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Description: SNAKE ADENOVIRUS 1 (SNADV1) WAS FIRST ISOLATED FROM THE CORN SNAKE ELAPHE GUTTATA, JUHASZ & AHNE, 1993, SEE ADDITIONAL REFERENCE 2. Production host: ![]() ![]() #2: Chemical | ChemComp-PE8 / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Sequence details | THE C-TERMINAL PART OF THE SEQUENCE IS DIFFERENT, WE BELIEVE THE DATABASE SEQUENCE IS WRONG. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 10 MM TRIS-HCL, 1.7 M AMMONIUM SULFATE, 0.085 M HEPES SODIUM SALT PH 7.5, 1.7%(V/V) PEG 400, 15%(V/V) GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2012 Details: CYLINDRICAL GRAZING INCIDENCE MIRROR BENT TO APPROXIMATE TO A TOROIDAL CURVATURE |
Radiation | Monochromator: LIQUID NITROGEN COOLED CHANNEL-CUT SILICON MONOCHROMATOR, SI(111) AND SI (311) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→70 Å / Num. obs: 113650 / % possible obs: 99.9 % / Redundancy: 11.9 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 6.5 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4D0V Resolution: 1.9→29.73 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.7 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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 mean: 32.1 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→29.73 Å
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Refine LS restraints |
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