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- PDB-3rkc: Hepatitis E Virus Capsid Protein E2s Domain (genotype IV) -

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Basic information

Entry
Database: PDB / ID: 3rkc
TitleHepatitis E Virus Capsid Protein E2s Domain (genotype IV)
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / Viral Capsid Protein
Function / homology: / Structural protein 2 second domain / : / Structural protein 2 C-terminal domain / viral capsid / identical protein binding / Capsid protein
Function and homology information
Biological speciesHepatitis E virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsTang, X.H. / Sivaraman, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural basis for the neutralization and genotype specificity of hepatitis E virus
Authors: Tang, X.H. / Yang, C.Y. / Gu, Y. / Song, C.L. / Zhang, X. / Wang, Y.B. / Zhang, J. / Hew, C.L. / Li, S.W. / Xia, N.S. / Sivaraman, J.
History
DepositionApr 18, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 3, 2013Group: Database references
Revision 1.3Nov 1, 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: Capsid protein
B: Capsid protein


Theoretical massNumber of molelcules
Total (without water)31,9782
Polymers31,9782
Non-polymers00
Water10,215567
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-18 kcal/mol
Surface area11700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.714, 66.533, 49.721
Angle α, β, γ (deg.)90.00, 107.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Capsid protein


Mass: 15988.812 Da / Num. of mol.: 2 / Fragment: UNP residues 93-240
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis E virus / Plasmid: pTO-T7 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: D3VV84
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 567 / 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: 2.21 Å3/Da / Density % sol: 44.29 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris, 20% PEG 10000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Nov 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. all: 26223 / Num. obs: 26223 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.6 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GGQ

3ggq


Resolution: 1.79→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1919 2432 9.3 %RANDOM
Rwork0.1548 ---
all-26281 --
obs-24882 --
Solvent computationBsol: 49.6549 Å2
Displacement parametersBiso mean: 13.3327 Å2
Baniso -1Baniso -2Baniso -3
1--2.089 Å20 Å20.786 Å2
2--1.301 Å20 Å2
3---0.788 Å2
Refinement stepCycle: LAST / Resolution: 1.79→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2240 0 0 567 2807
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_d1.736

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