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- PDB-7bv0: HEV-C E2s -

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Basic information

Entry
Database: PDB / ID: 7bv0
TitleHEV-C E2s
ComponentsProtein ORF2
KeywordsVIRAL PROTEIN / ORF2 / E2S
Function / homology
Function and homology information


host cell endoplasmic reticulum / T=1 icosahedral viral capsid / host cell Golgi apparatus / host cell surface / structural molecule activity / cell surface / RNA binding / extracellular region
Similarity search - Function
Hepatitis E virus structural protein 2 / Structural protein 2 nucleoplasmin-like domain / : / Structural protein 2 second domain / : / Structural protein 2 C-terminal domain / Viral coat protein subunit
Similarity search - Domain/homology
Pro-secreted protein ORF2
Similarity search - Component
Biological speciesHepatitis E virus
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsBai, C.Z. / Qi, J.X.
CitationJournal: To Be Published
Title: Structure of emerging human-infected hepatitis E virus E2s at 1.8 Angstroms resolution
Authors: Bai, C.Z. / Qi, J.X. / Wang, Q.H.
History
DepositionApr 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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Assembly

Deposited unit
A: Protein ORF2


Theoretical massNumber of molelcules
Total (without water)25,7731
Polymers25,7731
Non-polymers00
Water4,270237
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.660, 107.660, 75.458
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-302-

HOH

21A-383-

HOH

31A-426-

HOH

41A-475-

HOH

51A-506-

HOH

61A-528-

HOH

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Components

#1: Protein Protein ORF2


Mass: 25772.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis E virus / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3G1TVH2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 293.5 K / Method: batch mode
Details: 0.1 M sodium acetate trihydrate pH 4.5, 3.0 M sodium chloride

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: PAL-XFEL / Beamline: NCI / Wavelength: 0.988 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Oct 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 1.801→46.618 Å / Num. obs: 24297 / % possible obs: 99.74 % / Redundancy: 20 % / CC1/2: 0.75 / Net I/σ(I): 1
Reflection shellResolution: 1.801→1.8736 Å / Num. unique obs: 24297 / CC1/2: 0.5 / % possible all: 99

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GGQ

3ggq


Resolution: 1.801→46.618 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.73
RfactorNum. reflection% reflection
Rfree0.1881 1228 5.05 %
Rwork0.1709 --
obs0.1718 24297 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.67 Å2 / Biso mean: 22.7474 Å2 / Biso min: 10.15 Å2
Refinement stepCycle: final / Resolution: 1.801→46.618 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1169 0 0 237 1406
Biso mean---37.26 -
Num. residues----151
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8015-1.87360.22431450.2065244699
1.8736-1.95890.20311230.18142520100
1.9589-2.06220.18051350.16762506100
2.0622-2.19140.20151330.17582548100
2.1914-2.36050.19121210.18172540100
2.3605-2.59810.20031400.1792552100
2.5981-2.9740.19981490.18982558100
2.974-3.74660.18061350.16112627100
3.7466-46.6180.16891470.15462772100
Refinement TLS params.Method: refined / Origin x: -11.7706 Å / Origin y: -37.79 Å / Origin z: -9.1327 Å
111213212223313233
T0.0758 Å2-0.0078 Å20.0248 Å2-0.0769 Å2-0.0135 Å2--0.0806 Å2
L0.4592 °2-0.1264 °2-0.3107 °2-0.3098 °2-0.0068 °2--0.4786 °2
S0.053 Å °-0.0014 Å °0.011 Å °-0.0718 Å °-0.0019 Å °-0.0418 Å °-0.0259 Å °0.0519 Å °0.059 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA80 - 230
2X-RAY DIFFRACTION1allS1 - 237

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