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- PDB-2iny: Nanoporous Crystals of Chicken Embryo Lethal Orphan (CELO) Adenov... -

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Entry
Database: PDB / ID: 2iny
TitleNanoporous Crystals of Chicken Embryo Lethal Orphan (CELO) Adenovirus Major Coat Protein, Hexon
ComponentsHexon protein
KeywordsVIRAL PROTEIN / AVIAN ADENOVIRUS / CELO / MAJOR COAT PROTEIN / HEXON / CRYSTAL PACKING / NANOTECHNOLOGY / VIRAL JELLY ROLL / viral protein
Function / homologyAdenovirus Pll, hexon, C-terminal / Adenovirus Pll, hexon, N-terminal / Hexon coat protein, subdomain 4 / Group II dsDNA virus coat/capsid protein / Adenovirus hexon protein / Hexon, adenovirus major coat protein, N-terminal domain / Hexon, adenovirus major coat protein, C-terminal domain / T=25 icosahedral viral capsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral entry into host cell ...Adenovirus Pll, hexon, C-terminal / Adenovirus Pll, hexon, N-terminal / Hexon coat protein, subdomain 4 / Group II dsDNA virus coat/capsid protein / Adenovirus hexon protein / Hexon, adenovirus major coat protein, N-terminal domain / Hexon, adenovirus major coat protein, C-terminal domain / T=25 icosahedral viral capsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral entry into host cell / host cell nucleus / structural molecule activity / Hexon protein
Function and homology information
Specimen sourceFowl adenovirus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 3.9 Å resolution
AuthorsXu, L. / Benson, S.D. / Burnett, R.M.
Citation
Journal: J.Struct.Biol. / Year: 2007
Title: Nanoporous crystals of chicken embryo lethal orphan (CELO) adenovirus major coat protein, hexon.
Authors: Xu, L. / Benson, S.D. / Burnett, R.M.
#1: Journal: J.Virol. / Year: 2003
Title: Structural and Phylogenetic Analysis of Adenovirus Hexons by Use of High-Resolution X-Ray Crystallographic, Molecular Modeling, and Sequence-Based Methods
Authors: Rux, J.J. / Kuser, P.R. / Burnett, R.M.
#2: Journal: Mol.Ther. / Year: 2000
Title: Type-Specific Epitope Locations Revealed by X-Ray Crystallographic Study of Adenovirus Type 5 Hexon
Authors: Rux, J.J. / Burnett, R.M.
#3: Journal: J.Struct.Biol. / Year: 2006
Title: Capsid-Like Arrays in Crystals of Chimpanzee Adenovirus Hexon
Authors: Xue, F. / Burnett, R.M.
#4: Journal: Virology / Year: 1971
Title: Purification and Properties of Chick Embryo Lethal Orphan Virus (an Avian Adenovirus)
Authors: Laver, W.G. / Younghusband, H.B. / Wrigley, N.G.
#5: 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.
#6: Journal: J.Virol. / Year: 1999
Title: Mutational Analysis of the Avian Adenovirus CELO, which Provides a Basis for Gene Delivery Vectors
Authors: Michou, A.I. / Lehrmann, H. / Saltik, M. / Cotten, M.
#7: Journal: J.Virol. / Year: 1993
Title: Chicken Adenovirus (CELO Virus) Particles Augment Receptor-Mediated DNA Delivery to Mammalian Cells and Yield Exceptional Levels of Stable Transformants
Authors: Cotten, M. / Wagner, E. / Zatloukal, K. / Birnstiel, M.L.
#8: Journal: J.Virol. / Year: 1996
Title: Analysis of 15 Adenovirus Hexon Proteins Reveals the Location and Structure of Seven Hypervariable Regions Containing Serotype-Specific Residues
Authors: Crawford-Miksza, L. / Schnurr, D.P.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 9, 2006 / Release: Feb 6, 2007
RevisionDateData content typeGroupCategoryItemProviderType
1.0Feb 6, 2007Structure modelrepositoryInitial release
1.1May 1, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelDerived calculations / Version format compliance
1.3Apr 4, 2018Structure modelAdvisory / Data collectiondiffrn_source / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues_diffrn_source.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hexon protein


Theoretical massNumber of molelcules
Total (without water)106,7961
Polyers106,7961
Non-polymers00
Water0
1
A: Hexon protein

A: Hexon protein

A: Hexon protein


Theoretical massNumber of molelcules
Total (without water)320,3873
Polyers320,3873
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area (Å2)46140
ΔGint (kcal/M)-285
Surface area (Å2)103490
MethodPISA,PQS
Unit cell
γ
α
β
Length a, b, c (Å)157.770, 157.770, 114.200
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP 3 2 1
DetailsThe biological assembly is a trimer generated from the monmer in the asymmetric unit by the operators: -y, x-y+1, z and -x+y-1, -x, z

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Components

#1: Protein/peptide Hexon protein / / Late protein 2


Mass: 106795.633 Da / Num. of mol.: 1 / Source: (natural) Fowl adenovirus 1 / Genus: Aviadenovirus / Species: Fowl adenovirus A / Strain: Phelps Strain / References: UniProt: P42671

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.84 / Density percent sol: 67.97 %
Crystal growTemp: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 7% iso-propanol, 13% PEG 4000, 0.01 M glycine, 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 298 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Details: mirrors / Detector: IMAGE PLATE
RadiationMonochromator: YALE MIRRORS / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionD resolution high: 3.9 Å / D resolution low: 50 Å / Number all: 15294 / Number obs: 14636 / Observed criterion sigma I: 1 / Rsym value: 0.205 / NetI over sigmaI: 7.1 / Redundancy: 4.6 % / Percent possible obs: 95.7
Reflection shellHighest resolution: 3.9 Å / Lowest resolution: 3.97 Å / MeanI over sigI obs: 2.5 / Number unique all: 712 / Rsym value: 0.478 / Redundancy: 4.2 % / Percent possible all: 94.4

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Processing

Software
NameVersionClassificationContact authorContact author emailLanguageLocationTypeDate
CNS1.1refinementAxel T. Brungeraxel.brunger[at]yale.eduFortran_77http://cns.csb.yale.edu/v1.1/package
PDB_EXTRACT2.000data extractionPDBsw-help[at]rcsb.rutgers.eduC++http://pdb.rutgers.edu/software/packageApril. 3, 2006
CrystalClear(MSC/RIGAKU)data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1P30
Details: The structure was determined by molecular replacement using a model based on a threading of the CELO hexon sequence onto the human adenovirus type 5 hexon structure (1P30) using the program JACKAL; The residues that are consistent with the electron density are defined with an occupancy of 1, the areas that are disordered are designated with an occupancy of 0.
R Free selection details: RANDOM / Data cutoff high absF: 154406.875 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / Sigma F: 0 / Stereochemistry target values: Engh & Huber
Solvent computationSolvent model details: FLAT MODEL / Solvent model param bsol: 110.542 / Solvent model param ksol: 0.076
Displacement parametersB iso mean: 2.8 Å2 / Aniso B11: 2.44 Å2 / Aniso B12: -2.75 Å2 / Aniso B13: 0 Å2 / Aniso B22: 2.44 Å2 / Aniso B23: 0 Å2 / Aniso B33: -4.88 Å2
Least-squares processR factor R free: 0.416 / R factor R free error: 0.016 / R factor R work: 0.372 / Highest resolution: 3.9 Å / Lowest resolution: 47.06 Å / Number reflection R free: 710 / Number reflection obs: 14124 / Percent reflection R free: 5 / Percent reflection obs: 92.3
Refine analyzeLuzzati coordinate error free: 0.94 Å / Luzzati coordinate error obs: 0.59 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a free: 1.19 Å / Luzzati sigma a obs: 0.35 Å
Refine hist #LASTHighest resolution: 3.9 Å / Lowest resolution: 47.06 Å
Number of atoms included #LASTProtein: 7523 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 7523
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.300
X-RAY DIFFRACTIONc_dihedral_angle_d24.300
X-RAY DIFFRACTIONc_improper_angle_d1.000
Refine LS shellHighest resolution: 3.9 Å / R factor R free: 0.449 / R factor R free error: 0.045 / R factor R work: 0.314 / Lowest resolution: 4.14 Å / Number reflection R free: 100 / Number reflection R work: 2158 / Number reflection obs: 2258 / Total number of bins used: 6 / Percent reflection R free: 4.4 / Percent reflection obs: 89.4
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2

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