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

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Basic information

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
Function / homology
Function and homology information


T=25 icosahedral viral capsid / microtubule-dependent intracellular transport of viral material towards nucleus / host cell / symbiont entry into host cell / host cell nucleus / structural molecule activity
Similarity search - Function
Adenovirus Pll, hexon, subdomain 3 / Adenovirus hexon protein / Adenovirus Pll, hexon, N-terminal / Adenovirus Pll, hexon, C-terminal / Adenovirus Pll, hexon, subdomain 2 / Hexon, adenovirus major coat protein, N-terminal domain / Hexon, adenovirus major coat protein, C-terminal domain / Group II dsDNA virus coat/capsid protein
Similarity search - Domain/homology
Biological speciesFowl adenovirus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
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.
History
DepositionOct 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 4, 2018Group: Advisory / Data collection
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _diffrn_source.type
Revision 1.4Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
Polymers106,7961
Non-polymers00
Water00
1
A: Hexon protein

A: Hexon protein

A: Hexon protein


Theoretical massNumber of molelcules
Total (without water)320,3873
Polymers320,3873
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 area46140 Å2
ΔGint-285 kcal/mol
Surface area103490 Å2
MethodPISA, PQS
Unit cell
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-MP321
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 Hexon protein / Late protein 2


Mass: 106795.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / 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 Å3/Da / Density % sol: 67.97 %
Crystal growTemperature: 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 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.9→50 Å / Num. all: 15294 / Num. obs: 14636 / % possible obs: 95.7 % / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Rsym value: 0.205 / Net I/σ(I): 7.1
Reflection shellResolution: 3.9→3.97 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 712 / Rsym value: 0.478 / % possible all: 94.4

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT2data extraction
CrystalClear(MSC/RIGAKU)data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1P30

1p30


Resolution: 3.9→47.06 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 154406.875 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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 ...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.
RfactorNum. reflection% reflectionSelection details
Rfree0.416 710 5 %RANDOM
Rwork0.372 ---
obs-14124 92.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 110.542 Å2 / ksol: 0.076 e/Å3
Displacement parametersBiso mean: 2.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.44 Å2-2.75 Å20 Å2
2--2.44 Å20 Å2
3----4.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.94 Å0.59 Å
Luzzati d res low-5 Å
Luzzati sigma a1.19 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 3.9→47.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7523 0 0 0 7523
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d1
LS refinement shellResolution: 3.9→4.14 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.449 100 4.4 %
Rwork0.314 2158 -
obs-2258 89.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2

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