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- PDB-7er0: Crystal structure of capsid P domain of norovirus GI.3 VA115 -

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Basic information

Entry
Database: PDB / ID: 7er0
TitleCrystal structure of capsid P domain of norovirus GI.3 VA115
Componentscapsid P domain
KeywordsVIRAL PROTEIN / histo-blood group antigens / human norovirus / viral receptor
Biological speciesNorovirus GI.3
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.183 Å
AuthorsChen, Y.
CitationJournal: J.Virol. / Year: 2022
Title: Structural Insight into Terminal Galactose Recognition by Two Non-HBGA Binding GI.3 Noroviruses.
Authors: Wang, C. / Kang, H. / Tan, M. / Cong, J. / Su, D. / Li, X. / Chen, Y.
History
DepositionMay 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 3, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: capsid P domain
B: capsid P domain
C: capsid P domain
D: capsid P domain


Theoretical massNumber of molelcules
Total (without water)141,1784
Polymers141,1784
Non-polymers00
Water19,5461085
1
A: capsid P domain
B: capsid P domain


Theoretical massNumber of molelcules
Total (without water)70,5892
Polymers70,5892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-14 kcal/mol
Surface area23080 Å2
MethodPISA
2
C: capsid P domain
D: capsid P domain


Theoretical massNumber of molelcules
Total (without water)70,5892
Polymers70,5892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-15 kcal/mol
Surface area23300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.275, 60.001, 92.368
Angle α, β, γ (deg.)101.890, 97.730, 110.100
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
capsid P domain


Mass: 35294.613 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus GI.3 / Variant: VA115 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1085 / 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: 2.05 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 0.2M Sodium formate pH 6.4, 17% (w/v) Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.183→50 Å / Num. obs: 54367 / % possible obs: 94.1 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.036 / Rrim(I) all: 0.085 / Χ2: 2.297 / Net I/σ(I): 15.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.243.70.35419500.9510.1980.4082.65567.9
2.24-2.282.80.1424280.9510.0960.174.83684
2.28-2.324.20.29226430.9650.1540.3322.40891.2
2.32-2.375.70.19927100.9860.0910.2191.96294.2
2.37-2.425.70.18227410.9870.0840.2011.91694.5
2.42-2.485.70.18226860.9860.0840.21.92594.6
2.48-2.545.70.16327980.9880.0750.181.90295
2.54-2.615.70.14427410.9920.0660.1592.03595.1
2.61-2.695.70.13227420.9910.060.1452.0795.4
2.69-2.775.70.1227700.9930.0550.1322.09295.8
2.77-2.875.70.10427780.9950.0480.1142.13695.9
2.87-2.995.80.08927690.9950.0410.0982.14996.3
2.99-3.125.80.07928070.9960.0360.0872.21596.6
3.12-3.295.80.07127910.9960.0320.0782.32896.9
3.29-3.495.80.06428150.9980.0290.072.4697.2
3.49-3.765.10.06728170.9960.0330.0753.35997.3
3.76-4.145.10.0628070.9970.0290.0673.27997.6
4.14-4.745.80.04628250.9980.0210.052.33798.4
4.74-5.975.80.04628820.9980.0210.0512.11598.9
5.97-505.80.03928670.9990.0180.0431.93199.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P25

4p25


Resolution: 2.183→41.78 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.912 / SU B: 5.802 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.433 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2841 5.3 %RANDOM
Rwork0.1859 ---
obs0.188 51267 92.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.72 Å2 / Biso mean: 18.069 Å2 / Biso min: 4.57 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å2-0.63 Å2-1.77 Å2
2--0.05 Å2-0.18 Å2
3---0.22 Å2
Refinement stepCycle: final / Resolution: 2.183→41.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9227 0 0 1085 10312
Biso mean---24.09 -
Num. residues----1208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0139508
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178375
X-RAY DIFFRACTIONr_angle_refined_deg1.3251.64412994
X-RAY DIFFRACTIONr_angle_other_deg1.1781.56219555
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.74651204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.21523.19464
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.229151369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9761540
X-RAY DIFFRACTIONr_chiral_restr0.0540.21225
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210819
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021941
LS refinement shellResolution: 2.183→2.24 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.498 121 -
Rwork0.375 2496 -
all-2617 -
obs--60.48 %

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