+Open data
-Basic information
Entry | Database: PDB / ID: 1a92 | ||||||
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Title | OLIGOMERIZATION DOMAIN OF HEPATITIS DELTA ANTIGEN | ||||||
Components | DELTA ANTIGEN | ||||||
Keywords | LEUCINE ZIPPER / COILED-COIL / OLIGOMERIZATION / HEPATITIS DELTA / HDV | ||||||
Function / homology | Function and homology information virion component / viral penetration into host nucleus / symbiont entry into host cell / host cell nucleus / RNA binding Similarity search - Function | ||||||
Biological species | Hepatitis delta virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.8 Å | ||||||
Authors | Zuccola, H.J. / Hogle, J.M. | ||||||
Citation | Journal: Structure / Year: 1998 Title: Structural basis of the oligomerization of hepatitis delta antigen. Authors: Zuccola, H.J. / Rozzelle, J.E. / Lemon, S.M. / Erickson, B.W. / Hogle, J.M. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995 Title: Self-Association of a Synthetic Peptide from the N Terminus of the Hepatitis Delta Virus Protein Into an Immunoreactive Alpha-Helical Multimer Authors: Rozzelle Junior, J.E. / Wang, J.G. / Wagner, D.S. / Erickson, B.W. / Lemon, S.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a92.cif.gz | 52.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a92.ent.gz | 40.1 KB | Display | PDB format |
PDBx/mmJSON format | 1a92.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/1a92 ftp://data.pdbj.org/pub/pdb/validation_reports/a9/1a92 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein/peptide | Mass: 6006.051 Da / Num. of mol.: 4 / Fragment: OLIGOMERIZATION DOMAIN / Mutation: INS (K60-Y) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis delta virus / Genus: Deltavirus / References: UniProt: P25989 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.78 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.2 / Details: pH 5.2 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.15 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Jun 1, 1996 / Details: MIRRORS |
Radiation | Monochromator: CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.15 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→15 Å / Num. obs: 28279 / % possible obs: 94 % / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.038 / Net I/σ(I): 51 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.172 / Mean I/σ(I) obs: 7 / Rsym value: 0.2 / % possible all: 94 |
Reflection | *PLUS Num. measured all: 221286 |
Reflection shell | *PLUS % possible obs: 35 % / Rmerge(I) obs: 0.18 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.8→15 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 28.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.225 / Rfactor Rfree: 0.27 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 29.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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