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Yorodumi- PDB-2ium: Structure of the C-terminal head domain of the avian adenovirus C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ium | ||||||
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Title | Structure of the C-terminal head domain of the avian adenovirus CELO long fibre (C2 crystal form) | ||||||
Components | AVIAN ADENOVIRUS CELO LONG FIBRE | ||||||
Keywords | VIRAL PROTEIN / RECEPTOR-BINDING / AVIAN ADENOVIRUS / TRIMERIC PROTEINS / VIRAL FIBRES / BETA-SANDWICH / FIBER PROTEIN | ||||||
Function / homology | Function and homology information adhesion receptor-mediated virion attachment to host cell / virion component / viral capsid / symbiont entry into host cell / host cell nucleus Similarity search - Function | ||||||
Biological species | AVIAN ADENOVIRUS GAL1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.6 Å | ||||||
Authors | Guardado-Calvo, P. / Llamas-Saiz, A.L. / Fox, G.C. / van Raaij, M.J. | ||||||
Citation | Journal: J. Gen. Virol. / Year: 2007 Title: Structure of the C-terminal head domain of the fowl adenovirus type 1 long fiber. Authors: Guardado-Calvo, P. / Llamas-Saiz, A.L. / Fox, G.C. / Langlois, P. / van Raaij, M.J. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2006 Title: Crystallization of the C-Terminal Head Domain of the Avian Adenovirus Celo Long Fibre Authors: Guardado-Calvo, P. / Llamas-Saiz, A.L. / Langlois, P. / van Raaij, M.J. #2: Journal: J.Virol. / Year: 1996 Title: The Complete DNA Sequence and Genomic Organization of the Avian Adenovirus Celo. Authors: Chiocca, S. / Kurzbauer, R. / Schaffner, G. / Baker, A. / Mautner, V. / Cotten, M. #3: Journal: J.Mol.Biol. / Year: 1995 Title: The Avian Adenovirus Penton: Two Fibres and One Base. Authors: Hess, M. / Cuzange, A. / Ruigrok, R.W. / Chroboczek, J. / Jacrot, B. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ium.cif.gz | 148 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ium.ent.gz | 117.2 KB | Display | PDB format |
PDBx/mmJSON format | 2ium.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ium_validation.pdf.gz | 443.1 KB | Display | wwPDB validaton report |
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Full document | 2ium_full_validation.pdf.gz | 446.1 KB | Display | |
Data in XML | 2ium_validation.xml.gz | 32.9 KB | Display | |
Data in CIF | 2ium_validation.cif.gz | 50.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iu/2ium ftp://data.pdbj.org/pub/pdb/validation_reports/iu/2ium | HTTPS FTP |
-Related structure data
-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: 26486.662 Da / Num. of mol.: 3 / Fragment: C-TERMINAL HEAD DOMAIN, RESIDUES 579-793 Source method: isolated from a genetically manipulated source Source: (gene. exp.) AVIAN ADENOVIRUS GAL1 / Strain: TYPE 1 / Plasmid: PET28C-PLUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / Variant (production host): DE3 / References: UniProt: Q64787, UniProt: Q64761*PLUS #2: Water | ChemComp-HOH / | Sequence details | CRYSTALLIS | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.5 % Description: THE FILE R2IUMSF.ENT CONTAINS DETAILS OF THE MIR DATASETS USED FOR DETERMINING THE STRUCTURE. |
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Crystal grow | pH: 5.5 Details: 10-12% PEG 10000; 0.1 M HEPES-HAOH PH 4.7-6.1; 0-10% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.97986 |
Detector | Type: MARRESEARCH MAR165 / Detector: CCD / Date: Feb 25, 2006 / Details: FLAT AND TOROIDAL MIRROR |
Radiation | Monochromator: DOUBLE SI(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97986 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→25 Å / Num. obs: 88294 / % possible obs: 93.8 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.3 / % possible all: 73 |
-Processing
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Refinement | Method to determine structure: SIRAS / Resolution: 1.6→16 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.814 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.91 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→16 Å
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Refine LS restraints |
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