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- PDB-5e0i: Crystal structure of the HBV capsid Y132A mutant (VCID 8772) in c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5e0i | ||||||
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Title | Crystal structure of the HBV capsid Y132A mutant (VCID 8772) in complex with NVR10-001E2 at 1.95A resolution | ||||||
![]() | Capsid protein | ||||||
![]() | VIRAL PROTEIN / NVR10-001E2 | ||||||
Function / homology | ![]() 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 | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lukacs, C.M. / Abendroth, J. / Klumpp, K. | ||||||
![]() | ![]() Title: High-resolution crystal structure of a hepatitis B virus replication inhibitor bound to the viral core protein. Authors: Klumpp, K. / Lam, A.M. / Lukacs, C. / Vogel, R. / Ren, S. / Espiritu, C. / Baydo, R. / Atkins, K. / Abendroth, J. / Liao, G. / Efimov, A. / Hartman, G. / Flores, O.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 368.2 KB | Display | ![]() |
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PDB format | ![]() | 302.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4bmgS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17688.203 Da / Num. of mol.: 6 / Fragment: HBV CAPSID Y132A / Mutation: Y132A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: isolate United Kingdom/adyw/1979 / Production host: ![]() ![]() #2: Chemical | ChemComp-5J6 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 61 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M AMMONIUM CITRATE/CITRIC ACID PH 6.5, 9% ISOPROPANOL, 10% PEG 3350, 10% MPD, VAPOR DIFFUSION, TEMPERATURE 293K PH range: 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 14, 2013 |
Radiation | Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. all: 96089 / Num. obs: 95947 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.74 % / Biso Wilson estimate: 26.35 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 11.35 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 4.77 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 3.1 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4BMG Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.909 / SU B: 8.92 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.73 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→50 Å
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Refine LS restraints |
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