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- PDB-8j5b: Crystal structure of P domain from norovirus GI.4 capsid protein. -

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Basic information

Entry
Database: PDB / ID: 8j5b
TitleCrystal structure of P domain from norovirus GI.4 capsid protein.
Components(Capsid protein) x 3
KeywordsVIRAL PROTEIN / norovirus / p-domain / capsid
Function / homologyCalicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Capsid protein
Function and homology information
Biological speciesNorovirus Hu/GI.4/S50/2008/Lilla Edet/Sweden
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsKatsura, K. / Sakai, N. / Hasegawa, K. / Kimura-Someya, T. / Shirouzu, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: To Be Published
Title: Crystal structure of P domain from norovirus GI.4 capsid protein.
Authors: Katsura, K.
History
DepositionApr 21, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein


Theoretical massNumber of molelcules
Total (without water)132,5634
Polymers132,5634
Non-polymers00
Water7,945441
1
A: Capsid protein
C: Capsid protein


Theoretical massNumber of molelcules
Total (without water)66,6522
Polymers66,6522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-19 kcal/mol
Surface area22960 Å2
MethodPISA
2
B: Capsid protein
D: Capsid protein


Theoretical massNumber of molelcules
Total (without water)65,9112
Polymers65,9112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-19 kcal/mol
Surface area23110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.673, 62.791, 92.756
Angle α, β, γ (deg.)91.740, 97.710, 119.070
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Capsid protein


Mass: 33895.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/GI.4/S50/2008/Lilla Edet/Sweden
Gene: ORF2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9DU46
#2: Protein Capsid protein


Mass: 32756.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/GI.4/S50/2008/Lilla Edet/Sweden
Gene: ORF2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9DU46
#3: Protein Capsid protein


Mass: 33153.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/GI.4/S50/2008/Lilla Edet/Sweden
Gene: ORF2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9DU46
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 2.4 Å3/Da / Density % sol: 48.71 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M tri-Sodium citrate (pH5.6), 20%(v/v) 2-Propanol , 20%(w/v) Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→49.8 Å / Num. obs: 90970 / % possible obs: 95.9 % / Redundancy: 2.31 % / Biso Wilson estimate: 20.92 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.128 / Rsym value: 0.097 / Net I/σ(I): 6.98
Reflection shellResolution: 1.89→2.01 Å / Redundancy: 2.29 % / Mean I/σ(I) obs: 1.54 / Num. unique obs: 14442 / CC1/2: 0.849 / Rpim(I) all: 0.731 / Rsym value: 0.551 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→49.8 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.9 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2754 4600 5 %RANDOM
Rwork0.2321 ---
obs0.2342 87674 96.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.05 Å2 / Biso mean: 26.205 Å2 / Biso min: 8.24 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20.02 Å2-0.02 Å2
2--0.04 Å20 Å2
3----0.08 Å2
Refinement stepCycle: final / Resolution: 1.89→49.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9138 0 0 441 9579
Biso mean---27.68 -
Num. residues----1198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0139415
X-RAY DIFFRACTIONr_bond_other_d0.0350.0178255
X-RAY DIFFRACTIONr_angle_refined_deg1.5491.6512902
X-RAY DIFFRACTIONr_angle_other_deg2.3361.55919395
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.29851190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.524.05437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.715151356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.051532
X-RAY DIFFRACTIONr_chiral_restr0.0660.21238
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210619
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021801
X-RAY DIFFRACTIONr_mcbond_it2.1092.7424784
X-RAY DIFFRACTIONr_mcbond_other2.1082.7414783
X-RAY DIFFRACTIONr_mcangle_it3.2954.0935966
LS refinement shellResolution: 1.89→1.939 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 278 -
Rwork0.358 5268 -
all-5546 -
obs--78.18 %

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