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- PDB-5w1n: Crystal structure of the human astrovirus 2 Oxford serotype capsi... -

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Basic information

Entry
Database: PDB / ID: 5w1n
TitleCrystal structure of the human astrovirus 2 Oxford serotype capsid protein spike at 1.35-A resolution
ComponentsCapsid polyprotein VP90
KeywordsVIRAL PROTEIN / capsid protein / icosahedral virus
Biological speciesHuman astrovirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.348 Å
AuthorsBogdanoff, W.A. / Perez, E.I. / DuBois, R.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI095369 United States
CitationJournal: J. Virol. / Year: 2018
Title: Structural Basis for Escape of Human Astrovirus from Antibody Neutralization: Broad Implications for Rational Vaccine Design.
Authors: Bogdanoff, W.A. / Perez, E.I. / Lopez, T. / Arias, C.F. / DuBois, R.M.
History
DepositionJun 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.title / _citation.year
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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: Capsid polyprotein VP90
B: Capsid polyprotein VP90
C: Capsid polyprotein VP90
D: Capsid polyprotein VP90


Theoretical massNumber of molelcules
Total (without water)110,9264
Polymers110,9264
Non-polymers00
Water8,359464
1
A: Capsid polyprotein VP90
D: Capsid polyprotein VP90


Theoretical massNumber of molelcules
Total (without water)55,4632
Polymers55,4632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-6 kcal/mol
Surface area17740 Å2
MethodPISA
2
B: Capsid polyprotein VP90
C: Capsid polyprotein VP90


Theoretical massNumber of molelcules
Total (without water)55,4632
Polymers55,4632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-5 kcal/mol
Surface area17270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.630, 71.940, 92.810
Angle α, β, γ (deg.)90.000, 111.220, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Capsid polyprotein VP90


Mass: 27731.449 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human astrovirus 2 / Gene: ORF2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / 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: 1.93 Å3/Da / Density % sol: 36.12 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 0.2M Magnesium Acetate, 0.1M HEPES buffer.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033029 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033029 Å / Relative weight: 1
ReflectionResolution: 1.348→86.517 Å / Num. all: 177824 / Num. obs: 177824 / % possible obs: 96.3 % / Redundancy: 4.6 % / Biso Wilson estimate: 10.29 Å2 / Rpim(I) all: 0.053 / Rrim(I) all: 0.112 / Rsym value: 0.098 / Net I/av σ(I): 4 / Net I/σ(I): 10.4 / Num. measured all: 816628
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.35-1.424.40.3012.1112053251920.1540.3390.3014.893.6
1.42-1.514.50.2053.2109255243000.1050.2310.2056.495.5
1.51-1.614.50.1524.4104811231350.0780.1710.1528.196.8
1.61-1.744.70.1265.2101282217750.0640.1420.1269.997.7
1.74-1.914.80.0986.496831201570.0490.110.0981298.2
1.91-2.1350.0877.290942183310.0420.0970.08714.198.7
2.13-2.4650.0857.581387162640.0410.0940.08515.199
2.46-3.014.90.0777.767593137930.0380.0860.07715.599.1
3.01-4.263.90.0965.740161104090.060.1140.09614.396.7
4.26-43.9742.80.1084.81231344680.080.1360.1081275

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.35 Å43.97 Å
Translation1.35 Å43.97 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.22data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.22data extraction
Coot0.8.2model building
iMOSFLM7.1.1data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KOU

5kou


Resolution: 1.348→43.974 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 15.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1838 8967 5.04 %
Rwork0.1561 168830 -
obs0.1575 177797 96.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 52.5 Å2 / Biso mean: 16.0348 Å2 / Biso min: 4.71 Å2
Refinement stepCycle: final / Resolution: 1.348→43.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6942 0 0 464 7406
Biso mean---21.9 -
Num. residues----863
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077175
X-RAY DIFFRACTIONf_angle_d0.9629774
X-RAY DIFFRACTIONf_chiral_restr0.0841086
X-RAY DIFFRACTIONf_plane_restr0.0071243
X-RAY DIFFRACTIONf_dihedral_angle_d17.5832642
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.348-1.36330.21612840.16295347563191
1.3633-1.37940.20713000.15915429572993
1.3794-1.39620.2012810.15135472575394
1.3962-1.41390.18593190.14645498581794
1.4139-1.43250.17672880.13645532582095
1.4325-1.45210.18223070.1425543585095
1.4521-1.47280.18552510.14015607585895
1.4728-1.49480.19182810.13725609589096
1.4948-1.51820.18223090.1345586589596
1.5182-1.54310.16052940.12825607590196
1.5431-1.56970.17383120.12945647595997
1.5697-1.59820.17752920.1315716600897
1.5982-1.6290.18342940.12815683597797
1.629-1.66220.17363500.13185615596597
1.6622-1.69840.17183060.13115659596597
1.6984-1.73790.17863150.13035699601498
1.7379-1.78130.17442880.13525757604598
1.7813-1.82950.16613160.13325678599498
1.8295-1.88330.16543030.13295779608298
1.8833-1.94410.16693030.13165777608098
1.9441-2.01360.14513110.13475767607899
2.0136-2.09420.17872570.14025815607299
2.0942-2.18950.1753110.14555783609499
2.1895-2.3050.1772760.14945845612199
2.305-2.44940.18343110.16175820613199
2.4494-2.63850.18613030.1665811611499
2.6385-2.90390.18793550.16495764611999
2.9039-3.3240.17383120.17545810612298
3.324-4.18740.21242800.19155690597095
4.1874-43.99750.222580.21014485474375

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