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- PDB-5iyn: Protruding domain of GII.4 human norovirus CHDC2094 -

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Basic information

Entry
Database: PDB / ID: 5iyn
TitleProtruding domain of GII.4 human norovirus CHDC2094
ComponentsVP1
KeywordsVIRAL PROTEIN / Norovirus / Virus capsid / Protruding domain
Function / homology
Function and homology information


virion component / host cell cytoplasm
Similarity search - Function
Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit ...Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesNorovirus Hu/GII.4/CHDC2094/1974/US
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.56 Å
AuthorsSingh, B.K. / Hansman, G.S.
CitationJournal: To be published
Title: Four decades of structural evolution of GII.4 norovirus
Authors: Singh, B.K. / Hansman, G.S.
History
DepositionMar 24, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 2.0May 8, 2024Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.occupancy / _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: VP1
B: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,04411
Polymers67,4852
Non-polymers5599
Water11,187621
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint13 kcal/mol
Surface area22670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.190, 105.920, 135.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-1010-

HOH

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Components

#1: Protein VP1


Mass: 33742.633 Da / Num. of mol.: 2 / Fragment: P DOMAIN (UNP residues 225-530)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/GII.4/CHDC2094/1974/US / Plasmid: MBP-HTSHP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D0QJ68
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 621 / 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: 2.38 Å3/Da / Density % sol: 48.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: Sodium citrate, PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 27, 2015
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.55→48.14 Å / Num. obs: 92170 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 15.17 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Net I/av σ(I): 13.89 / Net I/σ(I): 14.04
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.55-1.590.7922.46195.7
1.59-1.630.663.28197.4
1.63-1.680.5044.46198.8
1.68-1.730.4025.57198.9
1.73-1.780.3166.91198.9
1.78-1.850.2468.46199.3
1.85-1.920.19210199.1
1.92-1.990.1511.7199
1.99-2.080.11413.65198.2
2.08-2.190.09815.38198.7
2.19-2.30.08217.67197.1
2.3-2.440.07319.77198.3
2.44-2.610.06521.75198.2
2.61-2.820.05723.83198
2.82-3.090.04826.23197.7
3.09-3.460.04229.42197.6
3.46-3.990.0431.13196.4
3.99-4.890.03833.84195.4
4.89-6.910.0434.59196.7
6.910.03933.92192.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.23 Å48.14 Å
Translation7.23 Å48.14 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IYN

Resolution: 1.56→48.137 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.76
RfactorNum. reflection% reflection
Rfree0.1752 4485 5 %
Rwork0.1517 --
obs0.1528 89726 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 68.36 Å2 / Biso mean: 19.4887 Å2 / Biso min: 6.03 Å2
Refinement stepCycle: final / Resolution: 1.56→48.137 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4682 0 36 621 5339
Biso mean--27.71 28.33 -
Num. residues----609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094905
X-RAY DIFFRACTIONf_angle_d1.2866722
X-RAY DIFFRACTIONf_chiral_restr0.053753
X-RAY DIFFRACTIONf_plane_restr0.007887
X-RAY DIFFRACTIONf_dihedral_angle_d12.5471747
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.56-1.57770.42031470.37492798294599
1.5777-1.59630.38521490.33772837298698
1.5963-1.61580.38981470.30792793294098
1.6158-1.63620.31241460.27332777292397
1.6362-1.65770.28321510.22972855300699
1.6577-1.68050.24421480.21092810295899
1.6805-1.70450.22671500.18712851300199
1.7045-1.72990.19921500.1822864301499
1.7299-1.75690.20181480.16342807295599
1.7569-1.78570.20171510.15982859301099
1.7857-1.81650.19231480.15922821296999
1.8165-1.84960.18511510.15272859301099
1.8496-1.88510.17671490.14882848299799
1.8851-1.92360.18141500.14512850300099
1.9236-1.96550.15481520.14212875302799
1.9655-2.01120.17081500.13692852300299
2.0112-2.06150.14791500.13672849299998
2.0615-2.11720.1631490.13772828297798
2.1172-2.17950.17581490.13322831298099
2.1795-2.24990.15721490.13122840298998
2.2499-2.33030.1651460.13352777292396
2.3303-2.42360.14071510.1382867301898
2.4236-2.53390.16631490.13792840298998
2.5339-2.66740.18751500.14452853300398
2.6674-2.83460.18161500.15362855300598
2.8346-3.05340.18461500.15662844299498
3.0534-3.36060.18031510.14482871302298
3.3606-3.84670.15311490.13452838298796
3.8467-4.84570.11861500.12222850300096
4.8457-48.16040.14881550.14452942309795

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