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- PDB-3ts3: Crystal structure of the projection domain of the turkey astrovir... -

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Basic information

Entry
Database: PDB / ID: 3ts3
TitleCrystal structure of the projection domain of the turkey astrovirus capsid protein at 1.5 angstrom resolution
ComponentsCapsid polyprotein
KeywordsVIRAL PROTEIN / virus protein / projection domain / astrovirus capsid
Function / homologyCapsid polyprotein VP90, C-terminal / C-terminal tail of astrovirus capsid projection or spike / symbiont-mediated suppression of host complement activation / Capsid, astroviral / Astrovirus capsid protein nucleoplasmin-like domain / T=1 icosahedral viral capsid / Viral coat protein subunit / Capsid polyprotein VP90
Function and homology information
Biological speciesTurkey astrovirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.49 Å
AuthorsDuBois, R.M. / Schultz-Cherry, S. / White, S.W.
CitationJournal: J.Virol. / Year: 2013
Title: Crystal structure of the avian astrovirus capsid spike.
Authors: DuBois, R.M. / Freiden, P. / Marvin, S. / Reddivari, M. / Heath, R.J. / White, S.W. / Schultz-Cherry, S.
History
DepositionSep 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Jan 15, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999Author states that these are natural sequence variations found in the strain of turkey astrovirus 2 ...Author states that these are natural sequence variations found in the strain of turkey astrovirus 2 from their lab.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid polyprotein
B: Capsid polyprotein
C: Capsid polyprotein
D: Capsid polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,65111
Polymers94,9784
Non-polymers6727
Water13,872770
1
C: Capsid polyprotein
hetero molecules

A: Capsid polyprotein


Theoretical massNumber of molelcules
Total (without water)47,5853
Polymers47,4892
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y+1/2,-z+21
Buried area5060 Å2
ΔGint-64 kcal/mol
Surface area16120 Å2
MethodPISA
2
B: Capsid polyprotein
D: Capsid polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0668
Polymers47,4892
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-76 kcal/mol
Surface area16360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.487, 127.878, 71.007
Angle α, β, γ (deg.)90.000, 104.490, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Capsid polyprotein


Mass: 23744.578 Da / Num. of mol.: 4 / Fragment: projection domain, UNP residues 423-630
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Turkey astrovirus 2 / Strain: strain 2 / Gene: ORF2 / Plasmid: pET52b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Q3G5
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 770 / 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: 2.06 Å3/Da / Density % sol: 40.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. all: 124890 / Num. obs: 124746 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.066 / Χ2: 1.004 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.49-1.544.70.391123620.878199.2
1.54-1.615.50.344124470.91100
1.61-1.685.70.263124370.9111100
1.68-1.775.80.204124700.961100
1.77-1.885.90.144124650.9661100
1.88-2.025.90.103125110.9811100
2.02-2.2360.075124751.0481100
2.23-2.5560.064124631.1251100
2.55-3.2160.06125301.2221100
3.21-5060.03125860.995199.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
SERGUIdata collection
HKL-2000data reduction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.49→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.246 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2053 6265 5 %RANDOM
Rwork0.1762 ---
all0.189 124890 --
obs0.1776 124665 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 49.9 Å2 / Biso mean: 13.1882 Å2 / Biso min: 2.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å2-0 Å2-0.14 Å2
2---0.13 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.49→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6599 0 35 770 7404
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226939
X-RAY DIFFRACTIONr_angle_refined_deg1.1791.9519485
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5945854
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.45624.189339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.622151131
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9761536
X-RAY DIFFRACTIONr_chiral_restr0.0840.21037
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215344
X-RAY DIFFRACTIONr_mcbond_it0.5691.54121
X-RAY DIFFRACTIONr_mcangle_it1.07626717
X-RAY DIFFRACTIONr_scbond_it1.59932818
X-RAY DIFFRACTIONr_scangle_it2.6044.52744
LS refinement shellResolution: 1.49→1.528 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 425 -
Rwork0.255 8527 -
all-8952 -
obs--98.2 %

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