+Open data
-Basic information
Entry | Database: PDB / ID: 3fd4 | ||||||
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Title | Crystal Structure of Epstein-Barr virus gp42 protein | ||||||
Components | Glycoprotein gp42 | ||||||
Keywords | VIRAL PROTEIN / C type lectin / herpesvirus / Virus entry / membrane fusion / Host-virus interaction / Lectin / Membrane / Transmembrane | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Human herpesvirus 4 (Epstein-Barr virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å | ||||||
Authors | Kirschner, A. / Jardetzky, T. | ||||||
Citation | Journal: Structure / Year: 2009 Title: Structure of Epstein-Barr virus glycoprotein 42 suggests a mechanism for triggering receptor-activated virus entry. Authors: Kirschner, A.N. / Sorem, J. / Longnecker, R. / Jardetzky, T.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fd4.cif.gz | 78.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fd4.ent.gz | 57.8 KB | Display | PDB format |
PDBx/mmJSON format | 3fd4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fd4_validation.pdf.gz | 439.1 KB | Display | wwPDB validaton report |
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Full document | 3fd4_full_validation.pdf.gz | 442.2 KB | Display | |
Data in XML | 3fd4_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 3fd4_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/3fd4 ftp://data.pdbj.org/pub/pdb/validation_reports/fd/3fd4 | HTTPS FTP |
-Related structure data
Related structure data | 1kg0S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 1
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-Components
#1: Protein | Mass: 21626.496 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human herpesvirus 4 (strain B95-8) (Epstein-Barr virus (strain B95-8)) Strain: B95-8 / Gene: BZLF2 / Plasmid: pbacgus-3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P03205 #2: 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: 2.01 Å3/Da / Density % sol: 38.74 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 9.5 Details: 30% PEG-3000, 100 mM CHES pH 9.5, 10 mM YCl3, 25 mM tris pH 7.5, 150 mM NaCl, temperature 298K, VAPOR DIFFUSION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.72505 |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 26, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.72505 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→46.73 Å / Num. all: 14237 / Num. obs: 14139 / % possible obs: 99.4 % / Observed criterion σ(F): 4.4 / Observed criterion σ(I): 4.4 |
Reflection shell | Resolution: 2.4→2.49 Å / % possible all: 99.1 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KG0 Resolution: 2.4→46.73 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 1 / SU B: 7.268 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.486 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.86 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→46.73 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1766 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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