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- PDB-3qsq: Crystal structure of the projection domain of the human astroviru... -

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Basic information

Entry
Database: PDB / ID: 3qsq
TitleCrystal structure of the projection domain of the human astrovirus capsid protein
ComponentsCapsid polyprotein
KeywordsVIRAL PROTEIN / receptor binding domain / astrovirus capsid
Function / homology
Function and homology information


T=3 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / host extracellular space / identical protein binding
Similarity search - Function
Turkey astrovirus capsid protein / Turkey astrovirus capsid protein / Capsid, astroviral / Astrovirus capsid protein nucleoplasmin-like domain / Viral coat protein subunit
Similarity search - Domain/homology
Capsid polyprotein VP90
Similarity search - Component
Biological speciesHuman astrovirus 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDong, J. / Dong, L. / Mendez, E. / Tao, Y.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Crystal structure of the human astrovirus capsid spike.
Authors: Dong, J. / Dong, L. / Mendez, E. / Tao, Y.
History
DepositionFeb 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2011Group: Database references
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid polyprotein


Theoretical massNumber of molelcules
Total (without water)27,2231
Polymers27,2231
Non-polymers00
Water2,468137
1
A: Capsid polyprotein

A: Capsid polyprotein


Theoretical massNumber of molelcules
Total (without water)54,4452
Polymers54,4452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3500 Å2
ΔGint-17 kcal/mol
Surface area17270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.374, 48.374, 167.098
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-61-

HOH

21A-119-

HOH

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Components

#1: Protein Capsid polyprotein


Mass: 27222.500 Da / Num. of mol.: 1 / Fragment: UNP residues 415-646
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human astrovirus 8 / Gene: ORF2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta 2 (DE3) / References: UniProt: Q9IFX1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.07 Å3/Da / Density % sol: 40.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 28% PEG 3000, 0.1 M CHES, 0.1 M glycine, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9794 Å
DetectorDate: Sep 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.8→55.7 Å / Num. obs: 21767

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→23.94 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.962 / SU B: 5.932 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2152 1115 5.1 %RANDOM
Rwork0.17971 ---
obs0.18142 20628 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20.33 Å20 Å2
2--0.67 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 1.8→23.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 0 137 1868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221903
X-RAY DIFFRACTIONr_angle_refined_deg1.2661.9272630
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4475243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.28624.42195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69215299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.403158
X-RAY DIFFRACTIONr_chiral_restr0.0940.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211511
X-RAY DIFFRACTIONr_mcbond_it1.0531.51133
X-RAY DIFFRACTIONr_mcangle_it1.84921882
X-RAY DIFFRACTIONr_scbond_it2.1323770
X-RAY DIFFRACTIONr_scangle_it3.2884.5732
X-RAY DIFFRACTIONr_rigid_bond_restr1.11831903
LS refinement shellResolution: 1.8→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 82 -
Rwork0.177 1482 -
obs--99.87 %

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