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Yorodumi- PDB-6t3z: Crystal structure of the truncated EBV BFRF1-BFLF2 nuclear egress... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6t3z | ||||||
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Title | Crystal structure of the truncated EBV BFRF1-BFLF2 nuclear egress complex | ||||||
Components | Nuclear egress protein 2,Nuclear egress protein 1 | ||||||
Keywords | VIRAL PROTEIN / Nuclear egress complex / Epstein-Barr virus / gamma-herpesviral core NEC | ||||||
Function / homology | Function and homology information host cell nuclear inner membrane / viral budding from nuclear membrane / membrane => GO:0016020 / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Epstein-Barr virus (Epstein-Barr virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55862788727 Å | ||||||
Authors | Muller, Y.A. | ||||||
Funding support | Germany, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: High-resolution crystal structures of two prototypical beta- and gamma-herpesviral nuclear egress complexes unravel the determinants of subfamily specificity. Authors: Muller, Y.A. / Hage, S. / Alkhashrom, S. / Hollriegl, T. / Weigert, S. / Dolles, S. / Hof, K. / Walzer, S.A. / Egerer-Sieber, C. / Conrad, M. / Holst, S. / Losing, J. / Sonntag, E. / Sticht, ...Authors: Muller, Y.A. / Hage, S. / Alkhashrom, S. / Hollriegl, T. / Weigert, S. / Dolles, S. / Hof, K. / Walzer, S.A. / Egerer-Sieber, C. / Conrad, M. / Holst, S. / Losing, J. / Sonntag, E. / Sticht, H. / Eichler, J. / Marschall, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6t3z.cif.gz | 171.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t3z.ent.gz | 115.6 KB | Display | PDB format |
PDBx/mmJSON format | 6t3z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6t3z_validation.pdf.gz | 440.7 KB | Display | wwPDB validaton report |
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Full document | 6t3z_full_validation.pdf.gz | 442 KB | Display | |
Data in XML | 6t3z_validation.xml.gz | 11 KB | Display | |
Data in CIF | 6t3z_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t3/6t3z ftp://data.pdbj.org/pub/pdb/validation_reports/t3/6t3z | HTTPS FTP |
-Related structure data
Related structure data | 6t3xC 5d5nS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 25967.768 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Epstein-Barr virus (strain GD1) (Epstein-Barr virus) Strain: GD1 / Gene: BFRF1, NEC2, HHV4-K4123Mi_BFRF1, NEC1 / Production host: Escherichia coli (E. coli) / References: UniProt: V5KTU9, UniProt: A0A2S1N254 |
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#2: Chemical | ChemComp-MLI / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.59 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop Details: The protein was dissolved in a buffer consisting of 50 mM TrisHCl, 150 mM NaCl, pH 7.5 and concentrated to values between 10-15 mg/ml. Diffraction quality crystals of BFRF1::BFLF2 were ...Details: The protein was dissolved in a buffer consisting of 50 mM TrisHCl, 150 mM NaCl, pH 7.5 and concentrated to values between 10-15 mg/ml. Diffraction quality crystals of BFRF1::BFLF2 were obtained at 4 degree C with 0.2 M sodium malonate, pH 4.5, 20% PEG 3350 as a reservoir solution. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.558→47.9 Å / Num. obs: 40577 / % possible obs: 59.64 % / Redundancy: 38 % / Biso Wilson estimate: 26.994976906 Å2 / CC1/2: 1 / Rrim(I) all: 0.1008 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 1.561→1.617 Å / Num. unique obs: 125 / CC1/2: 0.092 / Rrim(I) all: 0.2287 / % possible all: 3.18 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5d5n Resolution: 1.55862788727→44.2283333333 Å / SU ML: 0.178437412274 / Cross valid method: FREE R-VALUE / σ(F): 1.3436469259 / Phase error: 35.2978284248
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.0140751116 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55862788727→44.2283333333 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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