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- PDB-3kxs: Crystal structure of HBV capsid mutant dimer (oxy form), strain adyw -

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Basic information

Entry
Database: PDB / ID: 3kxs
TitleCrystal structure of HBV capsid mutant dimer (oxy form), strain adyw
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / Core protein / capsid / hepadnavirus / four helix bundle / icosahedral / dimer / Capsid protein / DNA-binding / Host cytoplasm / Host-virus interaction / Phosphoprotein / RNA-binding / Virion
Function / homology
Function and homology information


microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / viral penetration into host nucleus / host cell / host cell cytoplasm / symbiont entry into host cell / structural molecule activity / DNA binding / RNA binding / identical protein binding
Similarity search - Function
Hepatitis B viral capsid (hbcag) fold / Viral capsid, core domain supefamily, Hepatitis B virus / Hepatitis core antigen / Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHepatitis B virus subtype adyw
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsPackianathan, C. / Katen, S.P. / Zlotnick, A.
Citation
Journal: J.Virol. / Year: 2010
Title: Conformational changes in the hepatitis B virus core protein are consistent with a role for allostery in virus assembly
Authors: Packianathan, C. / Katen, S.P. / Dann, C.E. / Zlotnick, A.
#1: Journal: Biochemistry / Year: 2009
Title: A Mutant Hepatitis B Virus Core Protein Mimics Inhibitors of Icosahedral Capsid Self-Assembly
Authors: Bourne, C.R. / Katen, S.P. / Fulz, M.R. / Packianathan, C. / Zlotnick, A.
History
DepositionDec 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Revision 1.3Sep 6, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)96,3926
Polymers96,3926
Non-polymers00
Water3,747208
1
F: Capsid protein
E: Capsid protein


Theoretical massNumber of molelcules
Total (without water)32,1312
Polymers32,1312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-35 kcal/mol
Surface area14530 Å2
MethodPISA
2
C: Capsid protein
D: Capsid protein


Theoretical massNumber of molelcules
Total (without water)32,1312
Polymers32,1312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-32 kcal/mol
Surface area14050 Å2
MethodPISA
3
A: Capsid protein
B: Capsid protein


Theoretical massNumber of molelcules
Total (without water)32,1312
Polymers32,1312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-35 kcal/mol
Surface area14010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.162, 104.162, 86.917
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
DetailsAuthors state that the mutant is an assembly deficient dimer of core protein. The wt is also a dimer in solution but can be assembled into an icosahedron (PDB accession 2G33).

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Components

#1: Protein
Capsid protein / Core protein / Core antigen / HBcAg / p21.5


Mass: 16065.363 Da / Num. of mol.: 6 / Fragment: assembly domain residues 1 to 149 / Mutation: Y132A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis B virus subtype adyw / Genus: orthohepadnavirus / Species: Hepatitis B virus / Strain: ADYW / Gene: C / Plasmid: pET11c / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (DE3) / References: UniProt: P03147
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.82 Å3/Da / Density % sol: 56.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG1500, Calcium acetate, sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 18, 2009 / Details: mirror
RadiationMonochromator: Osmic Blue confocal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 228368 / Num. obs: 228368 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 41.8
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 5.34 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5refinement
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QGT

1qgt


Resolution: 2.25→25.32 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.931 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.294 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26418 2547 5.1 %RANDOM
Rwork0.21725 ---
obs0.21966 47650 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.25→25.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6724 0 0 208 6932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0226936
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.9639517
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2265844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.04622.862297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.267151030
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5121546
X-RAY DIFFRACTIONr_chiral_restr0.1210.21089
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0215330
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.121.54280
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.01326963
X-RAY DIFFRACTIONr_scbond_it2.91632656
X-RAY DIFFRACTIONr_scangle_it4.5494.52554
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.247→2.305 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 199 -
Rwork0.278 3506 -
obs--99.92 %

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