+Open data
-Basic information
Entry | Database: PDB / ID: 6cvk | ||||||
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Title | Hepatitis B e-antigen in complex with scFv e13 | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / HEPATITIS B / SINGLE CHAIN VARIABLE FRAGMENT / E-ANTIGEN / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information virus-mediated perturbation of host defense response => GO:0019049 / microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / : / viral penetration into host nucleus / host cell cytoplasm / symbiont entry into host cell / virus-mediated perturbation of host defense response / structural molecule activity / DNA binding ...virus-mediated perturbation of host defense response => GO:0019049 / microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / : / viral penetration into host nucleus / host cell cytoplasm / symbiont entry into host cell / virus-mediated perturbation of host defense response / structural molecule activity / DNA binding / RNA binding / extracellular region Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) Hepatitis B virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å | ||||||
Authors | Eren, E. / Steven, A.C. / Wingfield, P.T. | ||||||
Funding support | United States, 1items
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Citation | Journal: Structure / Year: 2018 Title: Structures of Hepatitis B Virus Core- and e-Antigen Immune Complexes Suggest Multi-point Inhibition. Authors: Eren, E. / Watts, N.R. / Dearborn, A.D. / Palmer, I.W. / Kaufman, J.D. / Steven, A.C. / Wingfield, P.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cvk.cif.gz | 311.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cvk.ent.gz | 254.3 KB | Display | PDB format |
PDBx/mmJSON format | 6cvk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cvk_validation.pdf.gz | 454.1 KB | Display | wwPDB validaton report |
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Full document | 6cvk_full_validation.pdf.gz | 461.7 KB | Display | |
Data in XML | 6cvk_validation.xml.gz | 30.8 KB | Display | |
Data in CIF | 6cvk_validation.cif.gz | 44.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/6cvk ftp://data.pdbj.org/pub/pdb/validation_reports/cv/6cvk | HTTPS FTP |
-Related structure data
Related structure data | 6cwdC 6cwtC 2kh2S 3v6zS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 26810.732 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Escherichia coli (E. coli) #2: Protein | Mass: 17865.424 Da / Num. of mol.: 2 / Mutation: C58A, C117A, E74D, M103V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis B virus / Gene: C, preC / Production host: Escherichia coli (E. coli) / References: UniProt: Q9QMH8, UniProt: L7R8Z1*PLUS #3: Water | ChemComp-HOH / | |
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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: 3.41 Å3/Da / Density % sol: 63.97 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 15% (w/v) PEG 550 MME, 0.1 M MES, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→20 Å / Num. obs: 44849 / % possible obs: 100 % / Redundancy: 5.1 % / CC1/2: 0.99 / Rpim(I) all: 0.072 / Rrim(I) all: 0.16 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.38→2.48 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4459 / CC1/2: 0.59 / Rpim(I) all: 0.58 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3V6Z, 2KH2 Resolution: 2.38→19.785 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.34 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.38→19.785 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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