+Open data
-Basic information
Entry | Database: PDB / ID: 4bmg | ||||||
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Title | Crystal structure of hexameric HBc149 Y132A | ||||||
Components | CAPSID PROTEIN | ||||||
Keywords | VIRAL PROTEIN / PROTEIN FOLDING / ALLOSTERY | ||||||
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 | ||||||
Biological species | HEPATITIS B VIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Juergens, M.C. / Alexander, C.G. / Shepherd, D.A. / Ashcroft, A.E. / Ferguson, N. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Thermodynamic Origins of Protein Folding, Allostery and Capsid Formation in the Human Hepatitis B Virus Core Protein Authors: Alexander, C.G. / Juergens, M.C. / Shepherd, D.A. / Freund, S. / Ashcroft, A.E. / Ferguson, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bmg.cif.gz | 342 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bmg.ent.gz | 286.2 KB | Display | PDB format |
PDBx/mmJSON format | 4bmg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/4bmg ftp://data.pdbj.org/pub/pdb/validation_reports/bm/4bmg | HTTPS FTP |
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-Related structure data
Related structure data | 3kxsS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 17358.785 Da / Num. of mol.: 6 / Fragment: RESIDUES 1-149 / Mutation: YES Source method: isolated from a genetically manipulated source Details: DISULFIDE LINK BETWEEN C61 RESIDUES AT THE DIMER INTERFACE Source: (gene. exp.) HEPATITIS B VIRUS / Strain: ADYW / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P03147 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.8 % / Description: NONE |
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Crystal grow | Temperature: 293 K / pH: 5.5 Details: 100 MM CITRATE PH 5.0, 15 % (V/V) ISO-PROPANOL, 1% (W/V) PEG 10 000, 293 K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.98 |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 6, 2013 / Details: TOROIDAL MIRROR (M2) |
Radiation | Monochromator: DCCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3→48.69 Å / Num. obs: 24745 / % possible obs: 95.3 % / Observed criterion σ(I): 1.8 / Redundancy: 1.8 % / Biso Wilson estimate: 79.77 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 3→3.08 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.8 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3KXS Resolution: 3→44.526 Å / SU ML: 0.5 / σ(F): 1.97 / Phase error: 37.63 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 96.54 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→44.526 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 37.4836 Å / Origin y: 2.0907 Å / Origin z: 19.9676 Å
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Refinement TLS group | Selection details: ALL |