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- PDB-1p30: Refinement of Adenovirus Type 5 Hexon with CNS -

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Basic information

Entry
Database: PDB / ID: 1p30
TitleRefinement of Adenovirus Type 5 Hexon with CNS
ComponentsHexon protein
KeywordsVIRAL PROTEIN / ADENOVIRUS / TYPE 5 / HEXON / VIRUS / JELLYROLL / COAT PROTEIN
Function / homology
Function and homology information


T=25 icosahedral viral capsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral capsid / symbiont entry into host cell / host cell nucleus / structural molecule activity
Similarity search - Function
Adenovirus Type 2 Hexon; domain 1 / Adenovirus Type 2 Hexon, domain 1 / Hexon Major Viral Coat Protein; domain 3 / Hexon Major Viral Coat Protein, domain 3 / Hexon Major Viral Coat Protein; domain 2 / Hexon Major Viral Coat Protein, domain 2 / Adenovirus Type 2 Hexon, domain 4 / Adenovirus Type 2 Hexon; domain 4 / Adenovirus Pll, hexon, subdomain 2 / Adenovirus hexon protein ...Adenovirus Type 2 Hexon; domain 1 / Adenovirus Type 2 Hexon, domain 1 / Hexon Major Viral Coat Protein; domain 3 / Hexon Major Viral Coat Protein, domain 3 / Hexon Major Viral Coat Protein; domain 2 / Hexon Major Viral Coat Protein, domain 2 / Adenovirus Type 2 Hexon, domain 4 / Adenovirus Type 2 Hexon; domain 4 / Adenovirus Pll, hexon, subdomain 2 / Adenovirus hexon protein / Adenovirus Pll, hexon, N-terminal / Adenovirus Pll, hexon, C-terminal / Hexon, adenovirus major coat protein, N-terminal domain / Hexon, adenovirus major coat protein, C-terminal domain / Group II dsDNA virus coat/capsid protein / Beta Complex / Distorted Sandwich / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHuman adenovirus 5
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRux, J.J. / Kuser, P.R. / Burnett, R.M.
Citation
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.
#1: 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.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: The refined crystal structure of hexon, the major coat protein of adenovirus type 2, at 2.9 A resolution.
Authors: Athappilly, F.K. / Murali, R. / Rux, J.J. / Cai, Z. / Burnett, R.M.
#3: Journal: ADENOVIRUS METHODS AND PROTOCOLS (IN: METHODS IN MOLECULAR MEDICINE, V.21)
Year: 1999
Title: Large-scale purification and crystallization of adenovirus hexon
Authors: Rux, J.J. / Pascolini, D. / Burnett, R.M.
History
DepositionApr 16, 2003Deposition site: RCSB / Processing site: RCSB
SupersessionNov 11, 2003ID: 1RUX
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 16, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE THE PROTEIN IS ACETYLATED AT THE N-TERMINUS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hexon protein


Theoretical massNumber of molelcules
Total (without water)107,9761
Polymers107,9761
Non-polymers00
Water5,477304
1
A: Hexon protein

A: Hexon protein

A: Hexon protein


Theoretical massNumber of molelcules
Total (without water)323,9293
Polymers323,9293
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area48550 Å2
ΔGint-280 kcal/mol
Surface area83690 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)150.700, 150.700, 150.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
DetailsThe biological assembly is a trimer generated by the operations z, x, y and y, z, x.

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Components

#1: Protein Hexon protein / / Late protein 2


Mass: 107976.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 5 / Genus: Mastadenovirus / Species: Human adenovirus C / References: UniProt: P04133
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.2
Details: 0.5 SODIUM CITRATE , pH 3.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Rux, J.J., (2000) MOL.THER., 1, 18.

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Nov 1, 1994 / Details: MIRRORS
RadiationMonochromator: double-mirror focusing system (Supper) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 39599 / Num. obs: 36549 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 14.6
Reflection shellResolution: 2.5→2.7 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 3 / % possible all: 87.6
Reflection
*PLUS
Num. all: 39573 / % possible obs: 92 %

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Processing

Software
NameVersionClassification
CNS0.9refinement
XDSdata scaling
CNS0.9phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RUX

1rux
PDB Unreleased entry


Resolution: 2.5→20 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1823 5 %RANDOM
Rwork0.158 ---
all0.158 39599 --
obs0.158 36549 92.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.4543 Å2 / ksol: 0.328156 e/Å3
Displacement parametersBiso mean: 26.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7000 0 0 304 7304
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.31
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it2.142
X-RAY DIFFRACTIONc_scbond_it2.132
X-RAY DIFFRACTIONc_scangle_it3.062.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.285 224 4.8 %
Rwork0.226 4478 -
obs-4702 71.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.309
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81

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