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- PDB-5kon: Protruding domain of GII.4 human norovirus isolate 08-14 -

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Basic information

Entry
Database: PDB / ID: 5kon
TitleProtruding domain of GII.4 human norovirus isolate 08-14
ComponentsVP1
KeywordsVIRAL PROTEIN / Viral capsid protein / Protruding domain / Norovirus
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
VP1 / Capsid protein
Similarity search - Component
Biological speciesNorovirus GII.4
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.51 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
DepositionJul 1, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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: VP1
B: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,02520
Polymers68,5082
Non-polymers1,51718
Water11,998666
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7860 Å2
ΔGint36 kcal/mol
Surface area23780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.640, 55.270, 86.810
Angle α, β, γ (deg.)90.000, 99.560, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein VP1


Mass: 34254.184 Da / Num. of mol.: 2 / Fragment: Protruding domain, UNP residues 225-530
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus GII.4 / Gene: KU985154 / Plasmid: MBP-HTSHP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0N9DUX3, UniProt: A0A172QPU7*PLUS
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 666 / 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: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG6000, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.979744 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979744 Å / Relative weight: 1
ReflectionResolution: 1.5→42.802 Å / Num. obs: 94115 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 10.23 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.84
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.5-1.540.5132.36192.6
1.54-1.580.4243.02199.8
1.58-1.630.363.55199.7
1.63-1.680.3034.2199.7
1.68-1.730.2475.05199.7
1.73-1.790.2036.14199.7
1.79-1.860.1637.65199.6
1.86-1.940.1319.35199.6
1.94-2.020.10111.89199.6
2.02-2.120.08114.41199.1
2.12-2.240.0716.36199.2
2.24-2.370.06218.3199.4
2.37-2.540.05719.6199.6
2.54-2.740.04921.65199.1
2.74-30.04324.09199.4
3-3.360.03329.5199.1
3.36-3.880.0332.65198.3
3.88-4.750.02536.8199.3
4.75-6.710.02433.68199.9
6.710.02130.93197.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.2 Å42.8 Å
Translation7.2 Å42.8 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.5.3phasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OOS

4oos


Resolution: 1.51→42.802 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.48
RfactorNum. reflection% reflection
Rfree0.1747 4644 5 %
Rwork0.1262 --
obs0.1286 92914 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 53.55 Å2 / Biso mean: 12.55 Å2 / Biso min: 3 Å2
Refinement stepCycle: final / Resolution: 1.51→42.802 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4804 0 96 666 5566
Biso mean--23.84 23.29 -
Num. residues----620
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115082
X-RAY DIFFRACTIONf_angle_d1.376931
X-RAY DIFFRACTIONf_chiral_restr0.082747
X-RAY DIFFRACTIONf_plane_restr0.007916
X-RAY DIFFRACTIONf_dihedral_angle_d12.7211841
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 (%)
1.51-1.52720.22861510.16162876302799
1.5272-1.54510.22971560.150629643120100
1.5451-1.5640.22131530.146929133066100
1.564-1.58380.22221560.14529573113100
1.5838-1.60460.21711520.143928933045100
1.6046-1.62660.21271560.139329643120100
1.6266-1.64980.24391540.137429213075100
1.6498-1.67450.21221560.143729603116100
1.6745-1.70060.23731520.135428863038100
1.7006-1.72850.20661570.129829923149100
1.7285-1.75830.1781540.124229243078100
1.7583-1.79030.19791540.123329163070100
1.7903-1.82470.19291550.116929433098100
1.8247-1.8620.17071540.117529243078100
1.862-1.90250.19711550.120229603115100
1.9025-1.94670.18561550.117129373092100
1.9467-1.99540.17461540.11852929308399
1.9954-2.04930.16481560.10932971312799
2.0493-2.10960.16711530.10822910306399
2.1096-2.17770.15681530.11162915306899
2.1777-2.25560.16321540.10832923307799
2.2556-2.34590.16641560.11332972312899
2.3459-2.45260.16811550.11642937309299
2.4526-2.58190.17711550.119929453100100
2.5819-2.74370.13471550.11672939309499
2.7437-2.95550.16271560.12642975313199
2.9555-3.25280.15371560.12722946310299
3.2528-3.72320.16131540.1322958311299
3.7232-4.68990.14541570.12432985314299
4.6899-42.81880.17041600.16033035319599

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