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- PDB-3tg7: Crystal structure of Adenovirus serotype 5 hexon at 1.6A resolution -

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Basic information

Entry
Database: PDB / ID: 3tg7
TitleCrystal structure of Adenovirus serotype 5 hexon at 1.6A resolution
ComponentsHexon protein
KeywordsVIRAL PROTEIN / Adenovirus structural protein / with new finding featuring possible binding to human coagulation factor X
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 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
Similarity search - Domain/homology
Biological speciesHuman adenovirus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsZhu, Y. / Roszak, A.W. / Isaacs, N.W. / McVey, J.H. / Nicklin, S.A. / Baker, A.H.
CitationJournal: To be Published
Title: crystal structure of Adenovirus serotype 5 hexon at 1.6A resolution
Authors: Zhu, Y. / Roszak, A.W. / Isaacs, N.W. / McVey, J.H. / Nicklin, S.A. / Baker, A.H.
History
DepositionAug 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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

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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
Water14,412800
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 operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area49450 Å2
ΔGint-313 kcal/mol
Surface area85150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.150, 149.150, 126.690
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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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 / References: UniProt: P04133
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 800 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 14% PEG 6000 in Bis-tris propane buffer., pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.57→45.55 Å / Num. obs: 138241 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.062

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0102refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P30

1p30


Resolution: 1.57→45.55 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.039 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22272 7132 5 %RANDOM
Rwork0.18384 ---
obs0.18578 135493 96.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.073 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å2-0.31 Å20 Å2
2---0.61 Å20 Å2
3---0.92 Å2
Refinement stepCycle: LAST / Resolution: 1.57→45.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7107 0 0 800 7907
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0227417
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3061.94410112
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2145911
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.20423.924367
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.693151163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1181545
X-RAY DIFFRACTIONr_chiral_restr0.1660.21071
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0215842
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5021.54517
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.29727324
X-RAY DIFFRACTIONr_scbond_it3.30232900
X-RAY DIFFRACTIONr_scangle_it4.7674.52786
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.568→1.609 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 526 -
Rwork0.258 10281 -
obs--99.54 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
1-4.126923.9771-46.2955
2-11.421-16.4884-15.8467
3-21.20839.5975-91.5856
43.3595-14.2224-97.8292
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A56 - 112
2X-RAY DIFFRACTION1A324 - 407
3X-RAY DIFFRACTION1A464 - 946
4X-RAY DIFFRACTION2A8 - 55
5X-RAY DIFFRACTION3A113 - 323
6X-RAY DIFFRACTION4A408 - 463

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